The PC (as a gaming platform) isn't as popular in Japan, sure - but that's not to say there's not Japanese games out there...
Japanese doujin / indie game-makers rate as the best Shmups out there.
http://www.tigsource.com/features/doujin-shmups.html
ABA games anyone?
http://www.asahi-net.or.jp/~cs8k-cyu/index_e.html
The indie scene in japan on the PC seems very strong, and they often recieve attention outside Japan.
Check out:
http://tigsource.com/articles/category/doujin
For a pretty extensive list of Japanese indie PC games out there
Cave story, which I've seen mentioned here before, is a translated Japanese endeavour
As for commercial games from large games developers, apart from the 'dating sims' which don't really have a market in the US or Europe, most of them do tend to be (often shoddy) ports from the console.
Much like many US commercial games for the PC from large games developers nowadays...