Anything with custom sprites will always be in my good books.
Pokemon Pebble Version got me into sprite comics and making sprites when I was about 9. Good humour and worth a read if your into pokemon comics http://www.pebbleversion.com/
Everybody knows DDSR of course, amazing comic and its great that RazorD9 has stuck with it over the years.
Kilobyte was a good comic with custom sprites, shame it ended last year.
Drunken Gunslinger is currently one of my favouriteshttp://drunkengunslinger.smackjeeves.com/
About 2-3 years ago there was a comic by somebody who used to go by the name The Sponge and SpongeMonkeyz called Shpam Man, very funny story about a spammer in the foruming world. Not sure what happened to it though.