Existential Comics
XKCD
Tiny Wooden Pieces
Sunday Morning Breakfast Cereal
Wondermark
Penguins and Logic
Chaospet: especially this Descartes comic and this Dennett Comic
Ph.D. Comics
Ted Rall's Website
The Nietzsche Family Circus
Dinosaur Comics
Cat and Girl
Cyanide and Happiness
Fantagraphics