KH recommendations
From ZooidWiki
Tokyo; two weeks - wow you will have lots of time. You know this may sound like a strange thing to recommend "while you're in Tokyo" and I don't know about your itinerary, but Kyoto is not all that far on the Shinkansen, and if you are not planning to see it otherwise, and your bookings are flexible, I would totally recommend getting out there for a day or two.
Otherwise - hmmn. All of these recollections based on 13 years ago - Shibuya, and when you're there try to find Tokyu Hands. It's an insane department store full of cool stuff (art supplies, weird hardware, etc.)
Shibuya itself is a necessary thing and I would say more important/cool than the Ginza (which you should also check out) - try to go so you're there (Shibuya) at night because that's when you'll see all the Blade Runner sort of insane sky-high neon and building sized TV screens best. http://en.wikipedia.org/wiki/Tokyu_Hands
Tokyo is a huge city - so if I were there for any period of time I'd try to map it out a bit by section, pick the things you know you want to see and then plan some exploring in those areas.
Some weird things I saw that not too many tourbooks will tell you about were Phillipe Stark's buildings in Tokyo. One, the Asahi Flamme D'or (also known by locals as kin no unchi (golden turd) or unchibiru (poo building) - is an insane bit of design amusement if you are in that area (Asakusa I think).
In Minato-Ku (which was a nice place to walk around and also where the Giger Bar was to be found, although I don't know if it still exists in any capacity) - is Stark's Nani Nani - unlike the Asahi beer hall it's not a publicly accessible building, but pretty weird nonetheless:
