We seem to be filling in the Egyptian pantheon:

Jacob = Sobek (check the alligator head and this: http://en.wikipedia.org/wiki/Sobek)
Richard Alpert = Ra
Horace Goodspeed = Horus
Locke = ? Going to guess Osiris

Sobek, Ra and Horus also seem to have a lot of dealings in Egyptian mythos, so they seem to 'fit' well together.

Beyond that ... not sure.

I wasn't happy with it. Not a lot happened for two hours except a few hippie gunfights (again). This season has been really strong, so the weak finale was a surprise -- I expected more.
Source(s):
http://en.wikipedia.org/wiki/Sobek

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I loved it.
What really surprises me about this series is how Josh Holloway and Terry Quinn have stolen the show. I thought that the characters of Jack and Kate would carry this show, but it is Sawyer and Locke who have captivated me, and Holloways performance in this episode was incredible.
Sawyer for all his toughness is, in reality, at the mercy of the the others around him. You see this in the expression of bewilderment on his face at the actions of Jack, Kate and Juliet. He is buffeted by their changing attitudes and plans. Although he teases Hugo, he actually feels more at ease in the company of the big guy.
For Sawyer, destiny is a lot less comfortable than normalcy.
The real mystery is John Locke. The man that looks like John Locke appears to be the man that was on the island at the beginning with Jacob.
And so we have wheels within wheels. The conflict between Ben and Charles Widmore is secondary to the real conflict between Jacob and the other guy.
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Ok, here's what I've been thinking, after looking into this a bit.

The Island has long been a character in and of itself. In many cultures, the Earth itself is envisioned as an island (sometimes on the back of a turtle, or another creature).

In ancient Egypt, Nit (Nieth) was the creator of all life, and the protector of Pharoah, Ra, and the god/ddess (s/he was androngenous) to whom the other gods came when they could not settle their disputes. She also guarded the coffin and associated canopic jars of one of the sons of Horus. S/he was the patron goddess of both war--and weaving. I am looking at her hieroglyphs for her name, and I think they may have been either on the wall in the underground area where the bomb was, or was on Jacob's weaving.

Isn't this what he was making?

http://upload.wikimedia.org/wikipedia/commons/b/bd/Egypt.Papyrus.01.jpg

That would be Anubis.

Ammit is another crocodile-headed god, whose job it was to judge the hearts of the dead. She was known as Devourer of Souls, but her function was to destroy evil. She was the guardian of the lake of fire. I'm thinking she's the smoke thing. I don't mean "Ammit is the smoke thing", but that somehow we'll find out that this is all Egyptian legend become real.

How that could happen is this: we know the Island can become shaken free of time and space. Perhaps at one time in the past, the island was in the Mediterranean, or off the coast of the Arabian Peninsula in the Arabian Sea.

According to Egyptian myth, at one point Osiris was killed and washed up on the banks of the Nile. What if he washed up on the banks of the Island instead?

According to the myth, then he was reanimated as Lord of the Dead.

I think Richard is Osiris in some way. Osiris was called "Ever Youthful", which we've noticed about Jacob; but it applies to both of them.

Then the rest makes sense: Horus, his son, was charged with protecting the people from Set, who killed Osiris and is thus both his enemy and Horus'. Set, incidentally, was Osiris' older brother, and the god of storms, darkness, and *necessary* chaos.

Horus would be Jacob. The legend also says that sometimes he would fail to recognize friends and mistake them for enemies, during the dark phase of the moon.

In the legend, Set and Horus had battles for years, so maybe I've got Osiris and Horus switched. But from last night's episode (the final episode of the season) this is a battle that's been raging for centuries, and this might finally be the last one.

There's an interesting little story about keeping a body in a box, too, when Set either tricked or put Osiris into a lead box that became his coffin. Only according to last night's episode and my reading of this, that would have been Set in the box.

Daniel Faraday's mother could possibly be Nephthys, sister/wife of Set, whose role it was to both guard Horus, and a very important role that included "gathering and mourning"--a mystical cycle crucial to the balance of chaos and order. She ages, though. So I'm not sure about this one, but it's a good parallel. Together with Juliet, they accomplished this season's goal. In the legend, it was Isis and Nephthys together who did the gathering and mourning.

So I think the background myth is from the whole Egyptian Underworld myth, and doesn't have much to do with other Egyptian gods like Ra.

I don't think that it's a straight retelling of the Egyptian religious myths, but a story that focuses on one of them and then brings other things in. Juliet, for example, has a lot in common with Isis. But she's not Isis: we know her parents divorced when she was around 10; that her sister had trouble conceiving. She ages. Daniel Faraday's mother ages.

So, I guess the series could be construed as: Part of the Egyptian pantheon were real (the ones associated with death). They are on a time-traveling island that appears on no charts. They handpick people to prove their respective points of good over evil/evil over good. The Oceanic Flight were hand-picked for the final battle, and it appears some of them were in the process of squaring off against each other. Only pairs of opposites like Bernard and Rose find peace; Kate/Jack/Sawyer/Juliet need to figure out which of them are going to pair off to find their place in the battle. Looks like they did in this episode; or maybe they got it wrong and that's why Juliet ended up at the bottom of the unbuilt hatch.

Next season? "They're coming" might refer to everyone coming back to life because the hatch was never built; it might refer to others in the Pantheon coming back to settle things. Hard to say.
Source(s):
http://www.touregypt.net/featurestories/nit.htm

http://ablemedia.com/ctcweb/consortium/ancientegyptiangodsneith.html

http://www.ancientegyptonline.co.uk/thegods.html

http://en.wikipedia.org/wiki/Duat

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Well, there's definitely stuff going on with Egyptian mythology...The presence of the Sobek statue and all the hieroglyphics (not to mention a character NAMED Horace/Horus) confirm that. But that opening scene also reminded me of the opening of Shakespeare's "The Tempest."

A "magician" of sorts, trapped on an island in exile, uses his powers to "call" on a ship. The castaways are then divided up into groups. Plots to overthrow Prospero are devised and abandoned, various other subplots are raised and thwarted, but all the time, Prospero is quiety influencing the main action and drawing the characters closer to him.

Similarly, "Jacob" is stranded on this island and manipulating those who pass through, though he's also locked in something of a rivalry with another god-like creature there.

Each season on "Lost" has set up this sort of binary conflict. We always think we're figuring out what the REAL rivalry is that's going on, only to find that it's more complex and mysterious than we thought...

Castaways vs. each other (Season 1)
Castaways vs. castaways from other side of the plane (Season 2)
Castaways vs. The Others (Season 3)
The Others vs. Dharma/Ben vs. Widmore (Season 4)
Jacob vs. Other God-like Being (Season 5)

My guess is Season 6 will continue this pattern...

Possibly:

Castaways vs. Other God-like Being (who's currently in possession of Locke's body, and probably has the ability to invade other dead people's bodies as well)

All the mention of some dark force that's "coming" could also be the final rivalry that we'll see play out, and even this playful back-and-forth among the gods is not the REAL FIGHT that's been playing out all this time. Perhaps Jacob and his rival are merely jockeying for position in preparation for some EVEN LARGER and more dangerous adversary that's still unknown to viewers.
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All the Egyptian stuff is mostly details...how the presence of other worldly beings was interpreted by early people's.

When it comes to the origin of the electromagnetic energy, the context of much of the context of Jacob's conversation with the other guy in the flashback, as well as Richard Alpert's long life and familiarity (though not by sight) with those folks who brought the crate with Locke's body to him....

Seems to me the explanation that makes the most sense is that a group of extraterrestrials crashed a very long time ago and there is no longer any surface indication of their craft on the island. That they're ship included a "black smoke" security system that attacks those of unclear motives who get too close to the ship or are potentially in conflict with the ETs.

Indigenous people's built temple's and worshiped them while the ETs have continuously brought groups of other humans to the island to demonstrate their "worthiness" and ability to exercise their choice and free will ...and this goes towards the ET's purpose.

There is a faction within the ETs that does not believe in human's potential and is tasked with exposing this weakness.

The extraterrestrial's, while very powerful and beyond human abilities, are not gods but able to inhabit human forms for their purposes, extending those human form's lives indefinitely, and or granting other humans healing or other abilities.

The extraterrestrials include Richard Alpert, Jacob, the other guy he was speaking with in the flashback, and likely all those who recently arrived carrying Locke's cargo crate to show Richard.

The Dharma construction breached a reactor of some sort, and the large Wheel that Ben turned was some part of a control to manage a time dilation field inherent in the ship's construction.

AND, the detonation of a nuclear device may not reset the time line of events as Faraday and Jack believe....depending on what fuels the drive for the extraterrestrial craft...anti matter? some much heavier radioactive isotope? a nuclear detonation may do a number of things including further scramble events and time lines, obliterate the planet, or provide the extraterrestrials with the evidence of human free will they may have been seeking provoking the arrival of a mothership for their return or to retrieve those few humans responsible for a greater mission.
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I loved the finale! It further confirmed why Lost is my favorite show.

I love what they did with Jacob, integrating him into the characters back stories, but I'm still wondering why he was there. Some had a point, like his meeting with Hurley, but others, like his meeting with Jack seemed insignificant.

I was shocked to fin out Locke was actually dead ever since Ben killed him. And it looks like the new Ben was that other guy in the form of a shape shifter. At least that's what I gathered. Ahh, now I gotta go back an rewatch it from that perspective.

I like that they answered a lot of questions, but like always, that bring up many more questions. So Jacob can live long like Richard and cannot be killed by that other guy, but Ben can kill him with a knife? I thought that was odd.

And now it looks like Juliet just detonated the H Bomb. Who know what kind of effect that will have.

Overall, awesome finale. The producers, writers, and actors of this show are amazing. Can't wait til next season!
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Just some reflections:

Black vs white. Good vs Evil. Faith vs Science. We continue to get this play of opposing forces throughout the story. Two mysterious men (Jacob and "Esau") - dressed in black and white discuss what sounds like some cosmic battle, some pattern, some endless loop they've been playing out through the ages. Are they demigods? Fallen angles? Or are they ordinary men - somehow caught up and displaced from the normal flow of time, space and physical laws by the island - doomed to relive a gruesome series of wars and battles that take place throughout the ages over control of the island? Could they have been soldiers or researchers from the US Army mission that once visited the island? They certainly seem to have some modern sensibilities despite their appearance hundreds of years ago watching as the Black Rock comes to the island.

The men speak of the endless violence - everyone comes to the island to kill one another and fight for control, and it always ends the same. But in the finale we are presented with an alternative - Rose and Bernard. They have simply chosen to live in peace and harmony. And they have been allowed to do so. Rose and Bernard are appearing more and more like the "Adam and Eve" found in the cave in season 1. Perhaps they are the only ones who come to realize that the island need not be a place of fear and death - it can be Eden - it is a matter of ones own choosing.

But the two men, they cannot seem to find peace. Must one of them die in order to break the holding pattern they find themselves in? We know that Jacob can leave the island, but can he ever be free of it? Is he like Jack, doomed and compelled to always return? And now that Jacob appears dead - now that the closing title has flipped from white on black to black on white - the power of the island has changed hands? Jacob, who we were lead to believe was the malevolent force, was depicted as a compassionate figure in this episode - weaving his way through the lives of the Losties - tugging at the threads like those in a loom in order to create a new pattern as he worked to help each one of them

Now that Jacob appears slain by the real force that has haunted the Losties from day one. The question is, who are "they" and how will they stop him?
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OMG the episode last night was totally awesome!!!! Well I couldn't sleep last night and I began to think of what might be the results of what was shown. I think the Miles may have been right. What they did by letting Jack put the bomb into the hatch may have been the reason of them being there in the first place. Miles' father got his hand injured and that could've cause him to have had his hand lost in the first place. I believe that things will still be the way they are even if Juliet were to have the bomb to explode. I think that the whole loop thing has been going on for awhile and maybe Jacob and the other character with him having been living life over and over again and have been trying to fix things ever since, that's why jacob has been trying to get things tied up together with getting everyone on the island to the points where they are suppose to be to that very moment. I'm pretty sure that they couldn't have fixed it because they still have one more season to go through. So, this may start all over again but with a few changes. Pieces of the puzzle with Jacob meeting everyone will finally be explained. But i believe that they are either going to forget one other which was their plan in the first place by setting off that bomb but somehow still have some memories of each other but vaguely. It'll be like a Donnie Darko ending. Or they will still be living out their lives on the island and continue their journey.
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I'll comment on the Jacob / Esau conflict and how Locke and Ben play a part. There are a lot of good comments already on other aspects.

From the argument that Jacob and Esau are having at the beginning of the episode, it appears that Jacob keeps bringing people to the island to try and work something out. Bringing the Black Rock to the island was just one moment in a long history. Esau believes it will never work and is looking for a loophole to kill Jacob.

Now we see Jacob interacting with the Losties before they ever come to the island. He is careful to touch each one of them and must be selecting them to come somehow.

Esau has been looking for his loophole and he has found it by taking on the appearance of dead people in order to manipulate those on the island. Jack's father, Christian, and now Locke. Richard thinks that "Esau in the guise of Locke" is the real leader, but actually that role has fallen back on Ben after the real Locke's death.

When they approach the statue, Richard complains that only the leader can come into Jacob's home, thinking that only Esau/Locke can come in. But Ben is the leader again and he is able to come in. Esau/Locke has manipulated Ben, the leader of the Others, to want to kill Jacob. This is the loophole - Ben doesn't realize that he is the real "Leader" and comes in to see Jacob because the rules allow him too and then stabs Jacob in an attempt to kill him.

Somehow, I think that despite the loophole that Esau has found, Jacob will not die from Ben's stabbing.
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