I think the ugliest ship(s) are the Miranda, Galaxy, Galaxy-X, Constitution, and Oberth.
Star Trek's ship designs didn't start to look good until they started streamlining the ships by removing the obnoxious neck that separated the hull and saucer. Even though the Oberth avoided having a neck, it's huge bulb for a saucer was just ugly.
Basically, the only ones that look good are all the escorts, the Intrepid, the Recon Science Vessel, the Assault Cruiser, Star Cruiser, the Atrox Carrier, whatever the Stargazer class cruiser is called because I don't want to look it up right now, and the Excalibur (The only exception I make to the necked cruisers.)
I only listed the Stargazer because thanks to it's customization options, I can make it look like a four-nacelled escort without the nacelles themselves sticking out too far from the rest of the ship.
"My frozen dairy-based confectionery attracts all the males of the species to the facilities. They all agree on it's superiority. Indeed, it is superior to yours. I could teach you the finer details but that would require monetary recompense on your part." -The Milkshake Song: Vulcan Edition
Looks like someone took and old school metal lunchpail and tacked warp nacelles on the thing.
Formerly known as Armsman from June 2008 to June 20, 2012
PWE Drone says: "Your STO community as you have known it is ended...Display names are irrelevant...Any further sense of community is irrelevant...Resistance is futile...You will be assimilated..."
Well, that's hard. Almost all FED escorts are ugly (except the Prometheus, perhaps with some of its variants), the heavy cruisers are ugly as well. The same goes for the Olympic class and its variants and the Oberth. Oh, forgot about the Deep space science vessels.
And there are many more single skins of otherwise nice ships.
But since I am to choose the ugliest, I'll go with the "escort", particularly the Ushaan skin.
On KDF side, there are many ships that I would call "interesting" instead of ugly, like the Kar'fi. So if I skip a couple single skins (Tor'kaht, among others), there remain the Guramba, the Marauder, the B'rel and the K't'inga... hmm, interesting, looks like I like KDF ships better. Anyway, the ugliest is hands down the Marauder flight deck cruiser.
TOIVA, Toi Vaxx, Toia Vix, T'vritha, To Vrax: Bring in the Allegiance class Toi'Va, Ti'vath, Toivia, Tia Vex, Toi'Virth: Add Tier 6 KDF Carrier and Raider. Tae'Va, T'Vaya, To'Var, T'Vira, To'Vrak: Give us Asylums for Romulans