It's really the mass market beyond the comic book stores where not having Moore's name attached will hurt. So, basically the collected editions. He's one of a handful of comic book creators that has some cache with non-comics readers in the booktrade, probably on par with Neil Gaiman. But I can understand -- he doesn't want to be associated with something that's been decades worth of headaches, not to mention published by Marvel (another source of headaches). In addition, when he signed the current contract, there was no guarantee that the work wouldn't be redrawn of mucked around in ways that were entirely outside of his control so why would he want his name on it? Anyway, his words and more horror stories (including one from Alan Davis) at:

http://comicsbeat.com/the-alan-mooremarvelman-interview-part-iii-i-definitely-wanted-my-name-taken-off-it/