I don't mean that one time when a game chugged to 5fps for 2 seconds, I mean a game that consistently over its length has the choppiest, least playable framerate. 

Bayonetta PS3.

I would have to say Skyrim for the PS3... it is by far the worst game in terms of Framerate issues and stalls/bugs that i have ever played... Still an amazing game though and played through tons of the quests and got the Platinum

Or maybe Need for Speed Undercover on Xbox 360.

Worst was Half-Life 2 on PS3.

Second worst was Dark Souls on PS3 (and it was not just in Blight Town).

Third worst was Two Worlds II on PS3.

Skyrim on PS3 actually runs smooth as silk.

Bayonetta on PS3 stood out for me too. I also got Avatar: The Game for free with my Wii, and it ran like a tortoise with arthritis at times.

I don't remember Mass Effect's framerate being bad, but I was probably just more tolerant back then; I find myself becoming much more attuned to framerates as time goes on, which can be annoying because it bugs me more now than it used to.

Bayonetta on PS3 hands down

Last Story on Wii was quite a pain in the ass.

Skyrim PS3
The Last Remnant - Still my fav game this gen
Black Site: Area 51
Mass Effect 1
Fable 1

Destroy all humans: Path of the Furon PS3
Skyrim PS3 (big save file)