As I mainly buy second-hand I tend to get most of my stuff from
Yahoo! Japan Auctions, as well as from people selling on the forums at
Soundtrack Central,
Chudah's Corner and
Slightly Dark. And for new releases,
VGM World,
play-asia and
amazon.co.jp are all good stores and at least one of them can usually get you what you're looking for.
I also used to use eBay a lot in the past, but these days I really only do so when someone from one of the above mentioned forums, or when someone I know is trustworthy, has something up for auction. To go and manually search that place for proper gamemusic these days is like searching for a needle is a... well - a swamp. And a real stinky one at that.
Most amazing jew boots
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seanne