Edit: The formatting! It burns!

Not all that many. There's:

* Darths & Droids: http://darthsanddroids.net/

* Everything else by those authors is also described (Irregular Webcomic!, Planet of Hats, mezzacotta, Square Root of Minus Garfield, Lightning Made of Owls, Comments on a Postcard, The Dinosaur Whiteboard, The Prisoner of Monty Hall, and Awkward Fumbles)

* Incomplete fan transcripts of The Order Of The Stick start at: http://oots.wikia.com/wiki/New_Edition

* XKCD transcripts are available from the Explain XKCD website, but I won't link them because the slogan, "Explain XKCD: it's 'cause you're dumb" assumes only stupid people need comic transcripts, and is thus rather offensive. Google it yourself.

* And don't forget the describer of Watchmen also describes Broodhollow: http://broodhollow.wikia.com/wiki/Book_1:_Curious_Little_Thing

And...that's all, really. If you're looking for more comic-like superhero stuff, you could also have a look at: http://unitedheroes.net/

But those aren't comics. They're just written stories about superheros.