This isn't a hardcore gamer's IQ test. It's a Photoshop stress test.
I know a good 90-95% of which games the characters come from, sadly enough, but I sure don't have time to through all that. Some fairly obscure ones in there, like Elevator Action, the original Spy Hunter car, Hobbes from Wing Commander 3(4?), the protagonist from Gods, and the ships from Star Control. (A sprite from the game that makes up my forum avatar would be even more obscure.)
Hey, shout out to including the Spelunky guy - who says an indy using Game Maker can't get some rep?
Oldest one is the cowboy from Boot Hill, assuming you haven't hidden a Space War sprite somewhere in there.
The gibbed corpse is on the Hitman's leg. It is indeed the pivotal example of the gibbed corpse.
Character that appeared in the most games: Mario. Oh, good God, Mario. Unless maybe you count the Arkanoid paddle as having cameos in every Arkanoid clone in existence.
Characters which are dead/watching eachother: trick question, inanimate character concepts are neither truly alive nor watching eachother. Hey, you did call it an IQ test.
A few I'm not sure count as a character. A guitar hero controller? Really?
Who's the space guy and gal standing behind Toejam and Earl? I don't know them, but looks like an interesting artistic style.