Sites i regularly go to that have completely blacked out their front page or blacked out their main content:
Wikipedia
VG Cats
xkcd
Dreamwidth (Okay, i don't go there that regularly, but i keep telling myself i should.)
Sites that had a large blacked out section or made some other obvious statement:
Questionable Content
Slashdot (At least if you normally check the site multiple times a day)
Livejournal
Sites that had a banner or statement of some kind, but not positioned prominently:
Penny Arcade
Amazon
LinkedIn (On their "LinkedIn Today" page, not really on the main page.)
Firefox/Mozilla, well, they have a news post about how they're going to do it, but my quick 30 second search didn't find any of the "key Mozilla websites."
Sites that are featured on Google's infographic as having publicly opposed SOPA and PIPA but who didn't do anything obvious on their main sites today to protest it, at least not as far as i can see. (Though to be fair, i am checking rather late in the day.)
Zynga
AOL
Ebay
