His run on Wally West's Flash series is, for me, by some margin, the best thing he's done. Overflowing with character and tremendous world building, punch-the-air moments and moments of absolute tragedy. He made Central and Keystone real, living places.
Close second, the first half or so of his Teen Titans run (up to about Infinite Crisis. I think the quality dip is excusable given the circumstances.) The work on the core four (Tim, Conner, Bart and Cassie) was excellent.
Green Lantern never did it for me, I'm afraid. The world building was a tremendous accomplishment, but I never felt it had the heart of some of his other work. Also felt it was more plot driven than character driven - you could have subbed in most other GLs as the lead and not a lot would have changed.
Superman and the Legion of Superheroes was excellent, too. He gets flack, but when Geoff is on his game he's really great.