I won't count lockbox/drop ships since I've never gotten one (Must...buy more...reinforcement packs!), here are mine:
Favorite (I mostly go by looks and "fun-to-play" rather than performance.)
1. Armitage - Had more fun in this ship than any other, and it combines the cool hotdog-bun saucer with the badass Akira layout. Also, the torpedo PDS is the best thing ever.
2. Chimera - Have yet to optimize it, but it's got the best gimmicks to gawp at. And a fish-face deflector is fun stuff.
3. Patrol Escort - Pretty much an Armitage without small craft, I love how much unlike any other feddie ship it looks. The Maelstrom Skin + Dervish Hull = lovely
4. Research Science Vessel - Considering how much combat there is in STO's war-torn galaxy, it's just hilarious to see the nerdiest-looking ship in Starfleet totally wrecking up fleets in the story missions.
5. Odyssey - It's the Enterprise! If I'm going to let any ship eclipse the sun, it'll be this behemoth. Playing with the basic free Oddy they gave out at the anniversary event was the most fun I've had in a cruiser, mainly because the ship's durability helps overcome my inability to play cruisers with any skill. Until I spring for an Atrox or Recluse, this is the only place I want to put beam arrays.
Honorary Mention: Vesta - I like the look, and it's probably OP as all hell (good for me when I buy it!) but it's not fair just to throw it in this list when it's not even out.
Least Favorite (I won't say "Worst" because this is mostly based on looks and "fun to play"):
1. Excelsior (Tier 3 version, not the Retrofit) - The first C-store purchase I regretted, because it taught me that I don't like how most cruisers play (pre-Odyssey). Honestly, I like the way the Excelsior looks, so this is really me being butthurt that a ship I can't fly well looks cool. Also, I'm super butthurt that the Retrofit version is still apparently one of the best ships in the Federation. I can't stand the idea that a 130-year-old design is outperforming the majority of spiffy new ships. Please, Cryptic, at least make a modernized version of the Excelsior skin so we can pretend it's a current model!
2. Regent - Another regret, because I spent 2500Z on this after I forgot that the only cruiser I like is my Oddy. Too slow for me to play like an escort, too squishy for me to play like an Oddy. It's pretty, though, and the wide-angle torpedo and metreon gas gimmicks are good times.
3. Deep Space Science Vessel - It's funny and a little sad that besides the Patrol Escort this is one of the more unique vessel designs in Starfleet compared to the rest, but once again, as the space whale of Science Vessels, I simply can't put it to decent use. Maybe picking up a Mirror Recon Science Vessel (which looks exactly like this one) will allow me to cross the gap.
4. NX-01 Replica - Despite it being a prequel ship, it looks more modern than the ships that came after, which I suppose is part of the reason why Enterprise was bad. That said, it does look good. Too bad its low-ass tier makes it not a great escort, since at its level most players won't be capable to playing with escort equipment or using escort tactics. Kind of a wasted opportunity, except for that grapple.
5. B'Rel BoP (starter version) - This isn't so much a knock against the BoP as it is a protest against the fact that the BoP is the very first ship Klink players get, and they end up playing it for quite a while until they get something new. Cryptic needs to rework the Klink campaign to offer starting KDF players a taste of what makes Klink ships different, how raptors, BoPs, cruisers and carriers play differently from the Escorts, SVs and Cruisers they're used to.