When it comes to story I prefer Something Positive, Dumbing of Age, Multiplex, A Comic with a French Name Involving Three People, GastroPhobia, The Zombie Hunters and Dead Winter. I love Something Positive so much, so addicted to it, that I have to forbid myself from reading till the end the year else I find myself antsy waiting for the next update.
As far as pure comedy goes I read Scandinavia and the World, Explosm, Saturday Morning Breakfast Cereal, Filibuster Cartoons, AmazingSuperPowers and Extra Ordinary. Usually avoid game related comics due to being tired of "This game's world doesn't match reality" or "This game is secretly scary due to X". Although I can't lie, that one comic of Dueling Analogs with Pac-Man envisioned as a supernatural cop thriller holds a special joy for me.