I mean none Temporal ships, so no Universe Class.
We have the Damar Cardassian Intel Science Dreadnought the Flag ship class for the Cardassian Union, the Scimitar Warbird the Flagship classes for the Romulan Republic, the Odyssesy Cruiser classes for the Federation, the Borq Battlecruiser Classes for the Klingon Empire, Jem'hadar Vanguard Dreadnought Cruiser.
These are just the ships that are stated to be the Flagships. I suspect one could include the Blackguard Assault Flight Deck Cruiser for the Orion Sydicate, The Kolosoi for the Nausicaans, the Multimission Gorn Ships for the Gorn, Bajoran Interceptor for Bajor, Sulik Assault Flight Deck Cruiser could all be called Flagships for there subfactions.
For me its hard but I'd make my list as follows.
1. Jem'hadar Vanguard Dreadnought Cruiser
2. Damar Intel Science Dreadnought (tough call, very close to first)
3. Scimitar classes
4. Odyssey ship classes
5. Borq Classes, I have heard alot of complaints about this class.
If you include the Blackguard I'd put it at number 3, but a close number 3.
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I currently prefer the Jem'Hadar Vanguard Warship over the Vanguard Dreadnought, precisely because it takes so much of makes the Scimitar work while replacing aspects that I didn't personally care for (the battle cloak and singularity powers) with a mechanic that I find easier to use (the wingmen).