Hi,
Here's my take on what one should do in three and a half days in the Megaopolis:
Inside Tokyo - daytime:
Asakusa - Sensoji, Kaminarimon and some interesting backstreet walks.
Harajuku - On weekends. If you stumble into Omotesando from here you'll also need a swivel for your head. The nice thing is you can visit the Meiji shrine (in the middle of a massive forest-park in the middle of Tokyo) and then visit something completely modern without too much effort.
Akihabara - Worth it just to spend some time in a maid cafe. You can probably kill an entire afternoon in the gargantuan Yodobashi Camera (Electronic megastore) if you have any interest in gadgets at all.
National Museum in Ueno: If you like museums and art galleries, this one is huge. Lots of stuff not in English, though. You can always stroll through Ameyoko market when you're done with it just to get an idea of what Tsukiji looks like.
If you want amusement parks, you can always check out the Sega Joyopolis' in Shinjuku and Odaiba, or just head to Disneyland. Friends of mine who were exhausted after a month of temples and traditional sightseeing in Asia did Disney Sea (there's a land, too) when they were in Japan just to have an easy day.
Things to do in the evening:
Walk around Shinjuku (Kabukicho). It's the red light district, and probably the most out of control place in Tokyo.
Roppongi - as a bit of a long termer, I tend to try and avoid Roppongi, though it's almost impossible to totally avoid it. Someone made a comment about the men/girl thing, which is wrong. Most of the girls, are girls in Roppongi, and I would even say they're definetely more "game" then the the gals you'll find in other districts (but they are there in a disproportionate number). Some good clubs in the area, and some bad. Azabu-Juban is a few minutes walk from Roppongi and has some better options, IMHO.
Shibuya - Younger and more Japanese than Roppongi. A really good place to catch live indie music - check the free weeklies when you're here to find out who's around.
Ebisu - nicer clubs, more relaxed pace, cool neighbourhood.
Capsule Hotel - grab one of these for a night if you get a chance.
Out of Tokyo (full daytrips):
Kamakura /Eno - Temples, huge Buddha and some nice coastal historical landmarks. My favourite daytrip for out of town guest who are from a place with mountains (as it's closer to the sea)
Nikko: Someone already mentioned this. A good option.
Fuji: The problem with Fuji is that you really need a car to get around the area effectively. If you come in winter you can see it clearly, but can't climb it, and if you climb it, you will need a full day. The only other thing is that if you come at any time outside of July and August, the mountain is closed to climbers, and the weather is typically unforgiving at higher altitues. The best thing about Fujiyoshida (the town at the base) is the insane rollercoasters at Fujikyu Highlands!
If you need any other info on what to eat, etc., let me know. I'll be here for a while yet.
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