i recomend kyoto for giesha and there is a small town nearby ( i forget the name, gomen) which is like samurai town. the entire place looks like something from the warring periods, complete with guys walking around as samurai. i think there's a ninja theme park, too >_>;
if you wanna go to tokyo, everyone knows akibahara is geek central; the train stop labeled tokyo has got the imperial palace, among other sights. Roppongi has a lot of clubs and nightlife, massage parlors (some happy ending, some not, pay attention to prices. if it is really high, its happy ending.), and its the closest exit to Tokyo tower, tho its still a bit of a walk. shinjuku and shibuya are also kinda famous, for the bussiest foot traffic in a road in the world, and the skyscrapper district.
not to far down the lines from tokyo is yokohama, a city with lots of malls, and the "sky garden", the veiwing deck on the tallest building in japan. on a clear day, you get a great view of mount fuji. it is beileved that if you dont climb mount fuji while you are here, you will come back. a bit further is kamakura, with lots of famous temples and shrines, including the giant buddha, and after kamakura is yokosuka, where i am
not much here compared to all the cities, but there is a lot more american stuff, and the two things near every base: bars and... okay, there are no strip clubs (that i know of) but lots of happy ending message parlors. oh, and shore patrol might think you are a sailor (if you're american, or american looking), and try to stop you from drinking after 11.
the subways are very easy to navigate, and if you have trouble, most people speak some kind of english. if you can pronounce where you are going, they will help. hell, if you so much as look confused, they might try and help, with or without you asking. there are also guys threwout the train stations at desks that can help you (they usaully even have little pocket maps of the train systems you can use). there are two major train companies ( i dont know thier names, its like jp and kiekyu, or something like that. theres almost always a store near the train stations, when you first get to the station, you would wanna go to the store, and ask the cashier for a "suica (su-ee-ka) card". there is another card for the otehr company, i dont know what its called, but they are interchangable. both railways accept the other's card. it will cost a little more than 2000 yen (like $20 give or take), and you can use it to get into/out of train stations. i recommend putting another 2000 or so yen on the card at the things that look like atms near the train station entrance. depending on which station it is, there will either be a red button to ask for help, or a little thing on the bottom left you can push aside, with a push-for-help button under it. if it is this kind, i warn you now, a guys head
WILL pop out of the wall right next to you. dont push it just to see it. theres also a push for english button, but i couldnt tell you where it is offhand. i beleive its on the upper left side. when you get to the the turnstiles, there is a a little square display with a picture of a suica card on it, you tap the card on this, and it will read the card and let you in. you exit the next station the same way. two last things, around seven-ish is rush hour on the trains. you will be packed in like a sardine, with guys wearing white gloves pushing everyone in. i'd avoid it, especially if you are a woman, and most definiatly if you are a blonde woman. the other thing is be aware of your surroundings. most japanese are extreamly polite, and try to act as the best hosts as they can (even if they must go way out of their way to help you, i've heard of them even going to a train station with you to make sure you get on the right connection) but there are always bad apples. im sure everyone knows of the groppers on the train; there are also hi-tech theives that can steal money off your suica card by waving a reader near your wallet (this nearly happened to me in shibuya)