First up, I agree with everything Psy mentioned.
Although I'm no expert on the city and plenty of others here know the place better than me, I have been to Tokyo a couple of times by myself and had an absolute blast but be warned, you will get lost, it's inevitable. But so what, every one gets lost there, it can be frustrating but also loads of fun, it's a great way to discover new things and see new places. But if you want to get back on track, so to speak, just keep walking until you find a train station or catch a taxi to the nearest one and go from there. Also, in my experience, Japanese people are incredibly helpful if you approach them for help.
Anyway, my personal tips for Tokyo off the top of my head that aren't mentioned in the list below, though I may well be stating the obvious at times....avoid the trains during peak hour [though the subway system isn't as complicated as some people make out,] announcements are also in English (usually), don't try and be polite and give way in fast moving crowds in the stations or on busy streets, you'll just cause problems, my advice is to look straight ahead and go for it, if there's a festival on, go to it, hang out in swanky department stores and be amazed and then eat some great, cheap food from the basement food courts [who knew the Japanese made the world's best potato salad?], and buy some chocolate whilst you're there, then go the bathroom and try all the buttons on the toilet but only while you're sitting down! if you see a 100 yen shop go in and buy stuff you didn't know you needed, ditto the Don Quixote stores, they are nuts, go to Yoyogi Park on a Sunday, visit Odaiba, Ginza, Ikebukuro, Ebisu, Koenji for tons of interesting little shops, Shinjuku, Shibuya, Meguro, Shiodome, Omotesando+Aoyama for luxury window shopping, Ueno and the Ameyoko market by the station but avoid the zoo in the park, ew-w-w-w, wander around Yanaka and check out the cemetery, hell, go anywhere it's all fun, buy watermelon on a stick, buy chicken on a stick, buy unagi on a stick, be prepared to get stared at but think nothing of it, you'll get used to it, be prepared to have someone fall asleep on you on the train, wonder at the cycling skills of young mothers with kids on the front and back, if someone offers you free tissues on the street take them, you'll need them, if there's a tray on the counter of the shop you're in put your money on that, check out j-pod's 'survival phrases' series before you go, ditto whatever lesson is it on how to reply when people tell you how good your Japanese is [don't say thank you, like I did, oh the shame], taxi doors open and close automatically [so don't upset the driver by trying to open them yourself, like I did], eat cheap ramen, eat cheap pasta at Pronto, excellent books at Kinokuniya behind Takashimiya in Shinjuku or 2nd hand at Good Day books in Ebisu, or if you're really into books go to Kanda Book town, be prepared to take countless photographs.....etc etc. But Tokyo is a truly fascinating place and it's possible to have an awful lot of fun very cheaply, it's certainly cheaper than Sydney where I live. Oh yeah, and try natto.
My favourite youtube Tokyo clip.
http://www.youtube.com/watch?v=Izq7Xqi48nA
First thing to do, buy one of these, it will make catching trains around Tokyo so much less hassle than buying tickets.
http://en.wikipedia.org/wiki/Suica
Handy web site, loads of information.
http://www.frommers.com/destinations/to ... 10001.html
More info.
http://www.tourism.metro.tokyo.jp/english/index.html
Pick up a free copy of this when you arrive.
http://metropolis.co.jp/default.asp
Loads of info about art galleries, exhibitions etc.
http://www.tokyoartbeat.com/event/
The guide book I would recommend.
http://www.timeout.com/travel/tokyo
The Tokyo street directory I would recommend.
http://www.kodansha-intl.com/books/html ... 25036.html
If you've got lots of money, here's a map for shopping.
http://www.superfuture.com/city/city/city.cfm?city=1
Watch the sunset and the city lights come on from here. Amazing.
http://www.roppongihills.com/tcv/en/
Or here (free).
http://www.metro.tokyo.jp/ENGLISH/TMG/outline.htm
A must see museum. Particularly the Honkan gallery.
http://www.tnm.go.jp/en/servlet/Con?pag ... ocessId=00
If you miss your cat.
http://www.mediatinker.com/blog/archives/008028.html
If you miss your dog.
http://www.tokyomango.com/tokyo_mango/2 ... now-d.html
Guide to parks/gardens. Ueno, Hama Rikyu and Skinjuku Gyoen being my favourites.
http://www.tokyoessentials.com/parks.html