Ohh..tough one.
The GTD Orestes stands out as one of my favorite designs. It's such a great blend of Terran functionality with Vasudan form, throws out some major hurt, carries an Admiral I'd like to punch in the face...
But, I just finished Diaspora (does that count for this discussion?) and the Theseus...oh how I fell in love with the Theseus. Galactica may get all the glory, but the Theseus (and Sobek-class in general) definitely got the looks. We didn't spend much time together (curse you short campaign!) but I absolutely adored everything about that ship. Fantastic gun coverage, plenty of launch tubes for Viper goodness, willingness to sacrifice dozens of pilots for a few useless civilian vessels.
My favorite SEXP is a much easier one - is-ship-stealthy. Not because of any actual usage, but whenever I see it I get this thought of a conversation the game engine is having with itself.
"Is it stealthy?"
"It's a Sathanas...it's over 6 kilometers long, what do you think?"
"Um...is that a yes?"
"NO! That's a NO! Why in the hell would you think a ship that huge could be stealthy?"
"Someone might have changed the flag..."
"Just die."
