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Origins and legends

Several possible origins are commonly given. The practice of blessing a sneeze, dating as far back as at least 77 AD, however, is far older than most specific explanations can account for.

One explanation holds that the custom originally began as an actual blessing. Gregory I became Pope in 590 as an outbreak of the bubonic plague was reaching Rome. In hopes of fighting off the disease, he ordered unending prayer and parades of chanters through the streets. At the time, sneezing was thought to be an early symptom of the plague. The blessing ("God bless you!") became a common effort to halt the disease.

A variant of the Pope Gregory I story places it with Pope Gregory VII, then tells the common story of "Ring Around the Rosey" being connected to the same plague.

A legend holds that it was believed that the heart stops when you sneeze, and the phrase "bless you" is meant to ensure the return of life or to encourage your heart to continue beating.

Another version says that people used to believe that your soul can be thrown from your body when you sneeze, that sneezing otherwise opened your body to invasion by the Devil or evil spirits, or that sneezing was your body's effort to force out an invading evil spirit. Thus, "bless you" or "God bless you" is used as a sort of shield against evil.

Alternatively, it may be possible that the phrase began simply as a response for an event that wasn't well understood at the time.

Another belief is that people used to see sneezing as a sign that God would answer your prayers or an omen of good fortune or good luck. In this case, "Bless you" would be in recognition of that luck.

Real Cause of a sneeze:

A sneeze (or sternutation) is a semi-autonomous, convulsive expulsion of air from the lungs at a minimum speed of 150 kph. Sneezing is usually caused by foreign particles irritating the nasal mucosa, but can more rarely be caused by sudden exposure to bright light or a full stomach. Sneezing is popularly considered to help spread disease in many cultures.
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The phrase "bless you" comes from the ancient belief that when you were sneezing demons were coming out of your body and "bless you" was the response people used to protect your soul. It is still used today because the phrase, sometimes without the reason why, has been passed down from generation to generation.

The website I've sourced also offers alternative explanations as to why people still say "bless you."
Source(s):
http://www.snopes.com/language/phrases/blessyou.asp

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I do not know what todays science says, but "God bless you" comes from the ancient belief that by sneezing you remove illness from your body. So there is something potentially wrong and you are on the best way to avoid it, especially with Gods blessing.

The Germans say "Gesundheit", meaning Health. Most of European languages have one of these two phrases, but both are based on the mentioned belief.

In my opinion this is a way of expressing affection for a fellow human. This how I feel when I am in ether position.

Matija
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If we don't say "bless you" after somebody sneezes, we are worried that, the other person might think "we are rude(not nice)".
Modern meaning could be:
"bless you" = "Thanks for covering your nose, when you sneezed. thanks for not spreading the germs!"
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At this point, it's just a social courtesy. Of course, we all know that no one really needs to be 'blessed' after a sneeze. We know they are not dying, possessed by evil spirits, or any other of the possible theories of origin.

However, the saying of "God bless you" which evolved to "bless you", for whatever reason, stuck as a form of common courtesy after a sneeze for centuries. Now, no one says it out of concern for the well-being of the sneezer at all, but instead out of their own concern of being viewed as impolite or simply out of habit.

I rarely say it myself because I think it's pointless, and I don't like the religious connotation. However, I do find myself saying it occasionally out of habit or in professional scenarios to be polite.

As a person who sneezes a lot, I find all of the sneeze blessings I receive somewhat annoying. How am I supposed to reply to those? I generally just say "thanks," but that seems so casual for a blessing response.

All of this sneeze talk reminds me of the episode of Seinfeld where Jerry proposes that he should replace "God bless you" after sneezes with a phrase that people will really appreciate: "You are so good looking!". I'm going to say this to anyone who sneezes around me today. It'll make them feel better than any blessing could!
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Although there are various theories about the origin, I think the reason so many people say it now is just "habit". Most people are not consciously blessing you--they are just responding in the way their mothers taught them...
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I was always under the impression that when people say "god bless you", and ancient believe was your body was expelling the "devil" out of your system, thus the saying "god bless you"

Of course we know its to expel and irritant of nasal mucosa receptors.
- Due to - rapid deep inhalation, pharyngeal constriction, and an air velocity near 115Km/hr. I have a test on this topic tomorrow hahah
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People say "bless you" because it's lingered in the culture as the appropriate thing to say. While you might find it strange and annoying, there are other people who'd find it impolite if it wasn't said! So even knowing that there isn't much reason to say it, it's perhaps best to go along with the tradition and not give offense needlessly. At least until you know what the person expects.

Pretty much all of our conversations are governed by these kind of cultural rules. Whether it's saying "Please" and "Thank you", or "Have a nice day", or "Wassup?" People from other cultures or subcultures who aren't raised to say those things find them equally strange, and possibly ridiculous or annoying!

It's even possible to cause people great offence by thanking them! :)
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Old habits die hard!
I have grown up using the Gazoontite (Gesundheit) method of response. I always loved the sound of that word and it takes away the stuffy orthodox sound of "bless you".
Sneezes were funny in my house growing up. My sneezes have always sounded like a mouse being expelled from a cannon, and people would always laugh at me.
Sometimes my brother would use the "bless you" approach, but mock it with a deep voice and adding ..."my child" afterward.
My sister would sometimes extend her sneezes with nonsensical words like, Achooo- ballo-mallo.
Maybe if we look at sneezing as performance art, it won't matter what a person says to you. And like @gno stated, we could clap at the end!
http://www.youtube.com/watch?v=NNYfZd8iV2k
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It's polite - customary. Manners are a nice thing to have around. Why all the fuss. ;-)
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