Have to categorize them I think.
Of the main/hero ships I think my least favorite is Voyager, I just always see an upside down spoon. I liked the original, more angular looking version much better.
Of the secondary ships (like Constellation, Nebula, etc) my least favorite is probably the Nebula. It has no sense of directionality to it. That's no doubt why they changed the mission module to an arrow-shape, to indicate "this way forwards".
Of the 3rd level ships, little seen, or kitbashes, the Yeager is pretty poor. Some of the Wolf-359 ships can be discounted as you can barely even see them on screen, they might as well have used some pieces of cardboard cut-out for most of the ones in the distance, would have saved the trouble.
As for my favorites.
Main ships. Enterprise-A, just lovely, perfect refinement of the original.
Secondary. Excelsior, has some really lovely long lines, and from the front looks very menacing, since it was an "adversary" ship in STIII this is perfect. Enterprise-C would be a close 2nd, have always liked the looks of it, and it looks good from multiple angles, well balanced.
Third. As far as the little seen or kitbashes, the Centaur type has nice lines, has much less of a jumble of parts type of feel to it.