On purely subjective and superficial grounds:
IRT: All IRTs look pretty good to me. But the R62/R62A is my favorite. Simple, understated, and reasonably comfortable.
BMT/IND: I like the R40 and R42--the slants for their general funkiness, and the R40M and R42 for their dinified simplicity. Something about the look just says "New York City".
My least favorite in terms of looks are the R44 and R46, mostly for the huge, monotonous grey breadbox exterior, but also for the the cramped seating arangement (very uncomfortable to sit forward or backwards if you have long legs), a problem shared with the R68. The R68 is a close second in the ugly department, though the shinier exterior makes the difference between a grey breadbox and a silver breadbox. Funny though, the R68 (and to a lesser the degree the R44/46) is somehwat similar in appearance to the R62, but its sheer size just makes the look ugly.
:-) Andrew