motor mount broken,
cylinder compression off due to a blown gasket,
dead cylinder,
cap and rotor worn incorrect or not firing cylinder,
damaged or malfunctioning spark plug or plug wire,
clogged fuel injector.
if its doing it at a stop light with the clutch not engaged could be anything i prevously stated while in gear and while moving, do a visual check of ur motormounts make sure nothings going on with them and u might want to do a compression check and see if somethign is wrong with one of the cylinders, and while ur engine is running pull the spark plug wire out, one at a time, if while u pull out one u dont notice a difference then for whatever reason the cylinder isnt firing, id say try those things and let me know the results, if u want download AIM and i can talk to u directly see if we can get anywhere.