Here's some ships from the top of my head
Kilrathi light carrier (picture on Making of WC3 CD)
Kilrathi cruiser (pic ditto as above, I would think it's a light cruiser, since the Fralthi II was already confirmed by the WC3 official guide to be a heavy cruiser)
Kilrathi scout frigate (game had a transport in place for it)
I don't know much on the Confed side. There wasn't a fleet/heavy carrier model in WC3 though, because the game was set on the Victory. The frigate model wasn't in there, but WC4 took care of that.
Prince Thrakhath's flagship was not in the engine model in WC2. The only cut Confed ship from WC2 that I know from the top of my head is the CVA Jutland-class. Unfortunately, compared to what I put in Fleet Tactics, I think I might have done an error in saying that CVA meant 'attack carrier', if the classifications in the WC Bible was anything to go by, the 'A' in CVA didn't mean 'attack', it meant 'armored with phase shields'.