I've been playing Uomoz's Corvus, so I hope I don't confuse people who are unaware of it.
Capital Ships:
Banshee Class- Lance of the Emperor, Blade of the Emperor
Jackhammer Class- Omnissiah, Deus Ex Machina
Titan Class- Adam, Eve
Sandstorm Class- Eschaton, Judgement Day, Exterminatus
Nausicaa Class- Astartes
Crusiers:
Aurora class- Ptolemios
Apogee Class- Void Walker, Orion's Belt, The Corsair
Pile Driver Class-Vanguard
Destroyers:
Medusa Class-Thermopylae, Daedalus, Icarus
Hammerhead Class- Theia, Rhea
Frigates:
Hyperion Class: Corsair, Gladiator
Tempest Class: Lady Luck, Miss Fortune, Thunderstruck
I tend to name my ships off of things from pop culture or history. Warhammer 40k makes an appearance, as well as biblical history and Greek/Roman gods and mythology. A lot of names come from my own sci-fi stories (I wrote a few for school projects/ contests).