I read 8-bit theatre, Misfile, and Fortuna Saga myself. I'm sure everyone's familiar with 8-bit, and I find Misfile rather entertaining. Basically an bit of a mixup with some paperwork in heaven leads to a boy becoming a girl (and all the past events of his life changing accordingly, though he still remembers the way his life should be), and a girl who was about to graduate high school and go to Harvard losing two years of her life and having to go back over it all again. It's a pretty good read and worth checking out.

The Fortuna Saga is hands down not only my favourite webcomic, but possibly one of the best pieces of fine literature I've ever read. Any FFVI fan should read it since it takes place in the year between the floating continent and Kefka destroying the world, and Celes waking up in the world of ruin. It doesn't involve the characters from the game though, and frankly I think is all the better for it (no matter how much I love FFVI). I can't stress enough how good this series is. It's not one of them there funny webcomics (though there is some humour every now and then); it's more serious with some of the best characters I've ever had the pleasure of reading about. Check it out.