Also some that I know of: Most of the Tales of Games have capability for Co-op Borderlands games Final Fantasy Crystal Chronicles Yoshi's Wooly World
There are plenty of co-op runs out there, its just a case of finding them
BattleBlock Theater Ibb & Obb Payday 2 Castle Crashers Left 4 Dead (1 & 2) Magicka (1 & 2) Terraria Newer Super Mario's (Wii and WiiU)
... just to name some
Searching like this may be something we can start to accommodate with the planned "game tags" update.
The real problem is finding people to play co-op with.
Speedrunning has always been a real time commitment, and practicing/schedualing with a friend is incredibly difficult. I have a hard enough time finding people on skype who want to play games normally. Granted i don't know what your friends circle is like, or if you stream. I prefer speedrunning on my own clock.