I've been a bit hesitant about replying to this thread as it seems my taste in music is somewhat different from that of the other posters... anyway, I'll start with the heavier stuff and work my way towards more mainstream bands.
One of the few truly original and innovative Japanese metal bands, and thus one of my very favourites, is Sigh. I particularly like Hail Horror Hail and Imaginary Soundscape albums, though the older stuff is pretty good too.
Church of Misery is an excellent old school doom metal band. Not very original, of course, but their songwriting is good enough that I'm willing to overlook that. Of the other "traditional" metal bands, Loudness and Sabbat both deserve a mention, if only for their sheer longevity. The bands play hard rock/heavy metal and trash metal, respectively. Not exactly groundbreaking material, but worth a listen or two if you're into that.
I'm not much into emocore as a genre, but Envy is a decent band and just the right cure for too much sugary pop tunes.
Tyrant is basically a Dimmu Borgir clone ("black metal" with lots of synths for those who don't know) and there are better bands in this genre in Europe, but I still listen to their Grimoires every now and then.
Of visual kei bands, I prefer the heavier bands (who'd have guessed...). D'espairsRay's Coll:set and Vidoll's Bijinkei often find their way into my cd player. Alice Nine and Kaggra, are both very good too (though I'd hard pressed to call Kaggra' "heavy").
Blood is an ok hard rock band. Not the visual kei band from Osaka, the one with Shinichiro Suzuki. I only have the album Noises, if anyone knows where to buy the others (short of ordering directly from the band), please let me know.
Moving to the softer stuff, Baroque is a good pop-rock band whose (sadly only) full length album, Sug Life hardly left my cd player last summer. And I guess I'll mention High and Mighty Color here as well...
And finally, since I believe it hasn't yet been mentioned in this thread, the best Japanese band ever and just the right thing for when you've listened to too much Envy; Under17.