KuBS holds a special place in my memory, as my first battleship ever in Freelancer multiplayer, on a different mod.
Also, Thannie, Bullhead, Theshie, Turtle.
Scylla is a very immersive ship, but after cloak nerf it became much worse.
Kronos would be one of my favourite vessels if it's stats would match the way it looks.
BHG Dessy, Bret Dessy, may be RM cruiser for capital ships, if you say PvP, valor also not bad.
For snubs, I'd say Manta, Odin, Titan, Sabur, and Wraith. I like those
Transports- Mastadont, for awesome look, Bison, for being hard nut, Kusari train, for being awesome too, and....all liners, I love them!