You can find some club suggestions in and around Roppongi here: http://hubpages.com/travel/Tokyo-Club-Spotlight
I'm still updating it, look back for more later.
Other nice things to do is the Early morning fish market, go to Odaiba, Shibuya is a good shopping district. Definately visit Harajuku and see the otaku-fashion on the bridge near omotesanndo. Go to Shinjuku and see the surrounding area there. Also check out Akihabara (otaku center) where there are lots of electronics and anima people. It really depends on what you are interested in? Culture, people, having fun?