Link and friends (nice site, but it's slow for me so I just visit the old site) and Zelda Comic were definitely my favorites, they are old though and they don't update that often anymore. Heroes Inc was also interesting.
Planet Zebeth always put a smile on my face. I like That's My Sonic and Ctrl-Alt-Del(I know, it's not a sprite comic, but it deserves mentioning) as well. White Ninja Comics are pretty good from time to time too.