I've actually never ridden a ride that's so rough I would consider it uncomfortable. The closest thing I've come though is colossus at thorpe which was very shakey in combination with too small restraints, my gf lost her earrings on that ride too...
Steel- Invertigo (KI) and Hypersonic XLC
Wood- Mean Streak and Thunderhawk (Dorney)
Flat- Crypt (for obvious reasons, apparently male HUSS employees don't test restraints on themselves or are poorly endowed)
^I wouldn't say Baco is the roughest coaster in the world, but certainly the most shakiest :?
But for me..
Steel: Corkscrew, and many other Vekoma's, absolute hell. Wood: Stampida (2007+), eughh kumbak trains... Flat: Probably some spinny fairground style ride, Waltzers normally give me whiplash, but I never really have problems with flats.