The Luna class iritates me, as looks good from some angles, but looks like a dog dragging itself across a carpet from others.
The golfball science ships qualify
Trident class Science ship - looks like a giant boot or a Vacuum cleaner or something.
And I'm sorry - I realise that this goes against popular opinion, and I don't hate it, but I find the Defiant class completely uninspiring. Again, this is my, personal, opinion, but it's nothing more than a saucer section with a nose-job and two nacelles shoved into it's side as an afterthought. I am aware of the supposed 'low profile' blah blah blah reasoning behind it but I'm sorry, I just don't like it much. Considering some of the concept art/designs for the class the end product just looks lazy and rushed.
Outside of STO - some of the DS9 Dominion war kitbashes were awful.
5th place- The Galor. They all look like they're flying backwards
4th place- Envoy- class cruiser. What were the designers thinking?
3rd place- Kar'fi carrier. It looks like a hybrid of a freight train and a catfish.
2nd place- The Olympic class sci and variants. I made mine with the clear sphere and called it theUSS Flying Fishbowl
and first place goes to...
The Breen Chel Grett Cruiser. That is the ugliest ship I've ever seen. If I flew one, I'd need a cloak just so no one would see me in it.
Smurf side it's a lot easier to just list the ships I do like because the rest are just generally hideous. However I do like the TOS Connie, Gladius, Class F Shuttle, and the Chimera is not too horrible, everything else is just Blech!
KDF side the worst of the offenders starts with the Kar'fi followed by the Hoh'SuS, K"Tanco, Marauder, Tor'Kaht, Korath, Krenn, and any Raptor design.
And let's not forget the horror known as the Galor.