If you want to know, like, what to do in Tokyo, there's a whole big internet out there. Browse my archives, check out the Nihon Sun, the Japan Travel page of About.com, the Tokyo Agenda listings at Metropolis, and Japan-i, for starters.
I figure you already have the big stuff in place - you know where to stay and have a few ideas about the main things you want to see. This is just a few tips to give you a little tiny edge as you're getting from place to place.
1. Get Tokyo City Atlas: A bilingual guide. I never left the house without this book for the first few months I was here. If we're friends, you can borrow one of mine. We have two.
2. Get a Pasmo card. Buy and load cash onto it at a machine at any train station. Even if you don't remember to get your $5 deposit back, it will be worth it in time and hassle saved calculating route prices and fiddling with tickets. And you'll get to see what the future feels like as you tap your wallet against the turnstile to get in and out of the train and subway system.
3. Walk on the left. This isn't a law or a rule or anything, but it took me a while to figure out why people were constantly bumping into me. Turns out, Japanese people are not necessarily clumsier than everyone else on earth, I was just wandering on the wrong side of the street. It seems obvious now, but it took kind of a while to figure out what was going on. Of course, you may be quicker than me.
4. Stand on the left. On escalators in the Tokyo area, stand to the left, walk on the right. (They say it's the opposite around Osaka.)
5. Watch your money. Pickpockets aren't a problem except maybe - maybe - if you're stumbling around Roppongi or Kabukicho late at night; running out of cash could be. The place is lousy with ATM's, but you will be surprised - and not in a good way - by how many of them won't take your non-Japanese ATM card. Or won't be open after a certain hour. Your best bet is often to use a Post Office ATM, but, even though the cash machines are often in a separate lobby that is partitioned from the main building, they usually shut by early evening. Any given convenience store chain's machine might or might not work with your particular card. They're all different, so if you find one that works for you, remember where it was.
6. Get an early start. If you must. Tsukiji market is not my favorite place, but people love it. The main tuna-auction action is over - already finished - before 6 am. It gets bright incredibly early and the trains are empty, so it feels like the city is extra supportive of your virtuous, seize-the-day zeal. Go get 'em. This will also make you feel better later when you...
7. Take a nap. Or a rest. Stop into a mom and pop coffee shop or a Starbucks or do like the salarymen and put your feet up in a massage chair for free at a big electronics store like Bic Camera or Yodobashi. Hang out on the grass at Yoyogi Park or on a bench at Koishikawa Kourakuen. The point is, just chill. You're not going to see everything anyway. You'll enjoy what you get to much more if you're rested. And I know that you could fly home first class if you had a dime for every time you were reminded of that, but it's one of those things that I know I need to hear again once in a while. So. Relax. Japandra's orders.
8. Get a late start. I am becoming more crowd-averse by the day. Bad luck, that, living in, you know, Tokyo. I hate popping out of the house at 8 on a Saturday morning to beat the crowds to wherever and finding out that 7 million other people had the same idea and they are all on my train. Where are they going? Why? Get to the famous museum or shop just as it's opening and enjoy a nice long line of fellow worm-getters. For the birds! Plan right, and hit the tail end of the lunch crowd, get to the museum an hour and a half before it closes, check out rooftop views at night. Get to the beach after the hottest part of the day and get the good spot that the sunburned family is already vacating. Go to a hot spring when people are at dinner and enjoy some quiet. Lots of karaoke places are open all day. Kill a few afternoon hours singing your head off at cheaper prices, then blink out into the evening just as lines are starting to form.
9. Don't miss the last train. They have "last trains," mostly somewhere around midnight. The theater of it can make it fun to ride the last train - the station staff wave and shout into megaphones and riders sprint and stumble for the gates as the warning bells ring - but it's no fun to miss it. Times are posted at the entrances of all the stations - glance at the sign as you're heading out for the evening. After that, you're looking at an expensive ride home, a long walk, or a lot of coffee and lousy pancakes at Royal Host. (This is not the worst thing in the world.) If you are into staying out all night at clubs or karaoke or a manga cafe, the last train is not a problem. You'll find the times the trains start up again on the same station signs.
10. Don't count on websites. I got into the habit in New York of jotting down just names to find out full details on places or items later. This isn't working so well here. A lot of really cool stores have functionless websites that are hard to find. If you like a place, be sure to grab a business card or catalog.
11. Talk to people. Ever had strangers share their cab with you, drop you off at your hotel, and refuse to take money for the fare just because you got yourself stranded at a rural train station after the buses stopped running? You won't believe how friendly and helpful people can be. You might not know a word besides "beer-u" and "arigatou" (you do know "arigatou," right?), but a good attitude and a little patience will probably get you anything you need. That, and maybe a little comical gesturing.
Bonus: Buy some stuff. You'll be glad when you got home. Try RanKing RanQueen for a little bit of everything, Don Quixote for a ton of everything, or, seriously, any convenience store. (See how that website had lots of useful English on the sidebar buttons, but then nary a word of it once you clicked through? Yeah. Key point: RanKing RanQueen is in Shibuya, Shinjuku, and Ikebukuro Stations.) Buy some goofy candy or black q-tips or t-shirts for your friends. Then, go back to that shop, spend a little extra, and get yourself that amazing thing you saw that will last a long time and remind you of your trip. When are you going to be back this way again?