It really depends on what it is you want to see.

If you want to see the local youth culture, then Shinjuku, Harajuku and Shibuya are the places to go.

There is also the Tokyo Metropolitan Building in Shinjuku.
It has an observation deck that is free and possibly the best view (outside of Odaiba) of Tokyo

It might be a good place to start because it has a tourist information center with pamphlets in English for everything you might want to see.

I live in Odaiba and I would spend one day checking out the sights there.
Things like a statue of liberty in Tokyo Bay, great view of Rainbow bridge, lots of colorfully lit boats in the bay at night. Also, if you come soon there is a gigantic life size Gundam in the park behind the shopping areas.
There is also the Palette Town Ferris wheel in Odaiba that is worth trying.

Getting to Odaiba and back is half the fun. There are two good ways to do it.
One is the Yurikamome line (http://en.wikipedia.org/wiki/Yurikamome)
that is a driverless automated bus/train of sorts. The other way is to walk across Rainbow Bridge.
It's quite a nice view and it's free.

For traditional Japan, then Asakusa is probably best.

Also you might check out the burial site for the 47 Ronin is interesting
(though it's not a full day destination, just an hour or two.)

Hope that helps get you started!
Source(s):
http://en.wikipedia.org/wiki/Tokyo_Metropolitan_Government_Building
odaiba
http://en.wikipedia.org/wiki/Odaiba
http://www.engadget.com/2009/06/12/life-sized-gundam-complete-and-no-you-ca...
http://en.wikipedia.org/wiki/Rainbow_bridge
http://en.wikipedia.org/wiki/Forty-seven_Ronin


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