Ahh, the memories.
Be sure to check:
http://www.japanimprov.com/index.html
and of course
http://www.tokyogigguide.com/
Record Stores:
http://www.psfmm.com/
http://www.warszawa.jp/
But there are also lots of cool small ones, you'll discover walking around.
Tower Records (i thing the biggest record store in Tokyo) could be interesting too, but i haven't been there.
Koenji is a fucking cool area: lots of bars and shops, second hand shops, etc.
Yoyogi Park and Harajuku for total weirdness. Lots of boutiques and and thousands of japanese hipsters.
I loved walking around the red light district at night.
Shinjuku, Shibuya and Akihabara, all amazing places.
In Kyoto Kiyomizudera is a must see. Beautiful Temples with view all over Kyoto.
Osaka is pretty cool too, especially around Namba area.
Nara is very nice, lots of deer and temples.
If you're going by train I'd check out the Japan Rail Pass, i think they are available for 1 and 2 weeks or so. You can't go with the superfast Shinkansen 3000 (or whatever it was called) but all the other JRail Shinkanses are included.
The fairy to Pusan (South Korea) is pretty cheap if you take the slow one (over night), so if you have enough time this could be interesting aswell.
Hey Slavo, hope you're fine.
Are you coming to Donaufestival this month?