I voted for SQ5 as well. It had a great supporting cast, and was probably the most fun to play. It was also very movie-like in it's presentation. Lots of dialogue, infiltrations, ambushes, rescues, awkward situations, etc.
SQ3 and 4 would come in after that for me. Those two seem to stand alone, placing the SQ series in a completely different self-referential reality where Roger can rescue his own creators and time is measured in sequels.
I've lowered SQ6 down my list a bit. It's still the funniest game by far, but the story seems to have too many holes in it and the characters are very under-used. I keep thinking Roger could've coerced Circuit Sydney into coming with him as a sidekick, and then kept salvaging Sydney for parts at every turn.
SQ1 and 2 - still classics, of course.