In addition to everyone that has been mentioned, I also think that Judd Winnick was underrated. He had his flaws, but he did a good job building up Kyle Rayner and his Outsiders run was enjoyable. I think he did his best work outside of superhero comics though and because most comic forums online that I've been to don't really seem to focus a lot on that he got a lot of crap when he was with DC. Exiles was also a good series.
While he's a novelist, I wish that Mat Johnson would've gotten to write more at DC. Right State and Papa Midnite never got much press but they were some of the more interesting comics from Vertigo.
I don't know if Jeremy Love has done more comics since Bayou but his work was a gem. It was the best of the webcomics on Zuda and one of the better works DC was putting out at the time. Looked really nice not just as a webcomic but as a comic in general too.