8-Bit Theater, a Final Fantasy sprite comic with frequent references to D&D.
Bruno the Bandit isn't really about gaming, but you'll find the staples of D&D anyway.
Elf Only Inn, although frequently on a hiatus, is comic about a fictionnal RPG IRC chatroom.
Irregular Webcomic is probably the geekiest webcomic you may find. Gaming (D&D, sci-fi, and super-heroes), Star Wars, Harry Potter, Indiana Jones, Cthulhu, and Steve Irwin. All that told with lego bricks and miniatures.
Mixed Myth features an adventuring party with a gynosphinx, a half-elf/half-goblin, a half-werewolf/half-selkie, and an alcoholic pooka (faerie horses). If that doesn't scream "D&D" to you, I don't know what will.
Order of the Stick is kinda obvious.
Penny Arcade and
PvP are sometimes related to RPGs, but they are not the primary focus.
RPG World is another webcomic about console RPGs.
Something Positive is not exactly a gaming comic, but RPGs (mainly D&D) is often referred to, and there is even a new D&D monster. (OK, the Redneck Tree isn't something you will want to use in game...)
The New Gold Dream is an unfrequently updated webcomic by the author of Something Positive.
A few people on these boards make their own webcomics to relate their campaigns.