AICN Anime made mention of the Eisner Awards for 2008, with some manga-themed material:
Best U.S. Edition of International Material — Japan
Cat Eyed Boy, by Kazuo Umezu (Viz)
Dororo, by Osamu Tezuka (Vertical)
Naoki Urasawa’s Monster, by Naoki Urasawa (Viz)
The Quest for the Missing Girl, by Jiro Taniguchi (Fanfare/Ponent Mon)
Solanin, by Inio Asano (Viz)
The one that people seem to be most hung up on is Cat-Eyed Boy, possibly because it's one of those titles people were not all that fond of to begin with. I know it's a "roots" title, but that doesn't mean it'll automatically garner an audience — but the award is about the quality of the adaptation and isn't strictly about the underlying material.One could argue that it would be better to give recognition to better titles overall, but then you get into the more difficult question of what the award category is really for. I like the fact that at least one of the Tezuka / Vertical reissues made it to the list, since just having his stuff in English at all is a blessing.
I plan to check out Cat-Eyed Boy at some point; for all I know the conventional wisdom about it could be completely wrong.