Okay its like this
Roppongi= Melting pot of foreigner's and Military crowd.
Shibuya= #1 spot of pure Japanese clubs.
Shinjuku=Small club scene.
Ageha= Biggest club in Japan.
Yokohama=Nice area but lot's of Navy guys.
Gaien=Rich people everywhere.
Further details about the area's...
Roppongi is pretty much the place to go if you just wanna be in a club and don't to much when it comes to quality of girls or the environment for that matter. Roppongi used to be really nice when Velfarre and Vanilla were open but they got shut down. So the only good place left is Flower. Of course you have various bar's and such but again there is alot of foreigner's and military crowd and not so much japanese.
Shibuya is pretty much either house music or Pop. They do play hip hop at some clubs such as Asia, Womb, Harlem, 27 Destiny, Vuenos. The girls IMO are way better looking and they take better care of themselve's. Most clubs will not let you in without your Stateside ID or your Passport so make sure you bring that along. ***MUST READ*** If you do plan on going to a club in Shibuya make sure you have a Japanese guest with you. Reason being they don't let foreigners in without a Japanese person to take you in with them as your guest, the reason for that is because foreigners have been known to start fights. So if you get into a fight your banned from the club and so is the japanese person who escorted you.
Shinjuku is not so much on the club side but more bars and pubs. So if your into that kinda thing you should feel right at home. Also alot of buisness people meet here to drink so you'll see alot of guys in suits drunk off their ass walking around laughing(It can be comical at times).
Ageha...*Sigh*Good times... it cost roughly about 4000 Yen just to get in but the place is so damn huge and it has so many dance halls in it that you'll be glad you paid once you get in. They don't play just one type of music in fact Hip Hop has the smallest section. House/Trance/Techno have the biggest sections followed by Reggae...
Yokohama has a more upscale kinda feel to it as far as clubbing goes. However with the Navy guys running around alot of places don't let foreigners in becase of the same reason in shibuya "Fights". They do have their rundown area's though so don't get mislead.
Gaien is pretty much where you would expect Paris Hilton to be. Most clubs cost around 10,000 Yen to get into and they enforce a strict dress code. Don't know to much about it because i never cared to spend that much just to get into a club, but atleast you know what you take home from their won't be a broke...
So in all fairness i recommend going to Shibuya. I've had the best times their and the environment is good. If you ever get the chance though head to Nagoya and go to "Club iD" Brazilian girls and Japanese girls nuff said...
Agree with the Shibuya beign the best in Tokyo....however that last statemetn about CLub ID is pretty off, lived in Nagoya for 6 months and I must says its teh worst club I`ve been to in Japan unless you are really into techno/european crap music and sketchy white dudes alll over the place..Don`t go there. hit up one of the many smaller hip hop clubs instead. granted it wont be as many people but you wont have to deal with slimy gaijin all over the place.