As comics become more accepted, we see more mainstream awards covering them. The Bram Stoker Awards are from the Horror Writer’s Association. The Stoker’s have added a graphic novel category and the nominees were recently announced:
Brosgol, Vera — Anya’s Ghost
Hill, Joe — Locke & Key, Volume 4
Jensen, Jeff — Green River Killer
Maberry, Jonathan — Marvel Universe vs. Wolverine
Mignola, Mike and Golden, Christopher — The Plague Ships
Moore, Alan — Neonomicon
You’re probably more familiar with the Mignola/Golden entry as Baltimore: The Plague Ships.
The (fan-based) Hugo Awards have had a comics category for a few years now. It wouldn’t surprise me if the Edgars (Mystery Writers of America) added a comics category one of these years, since they recognize the format.