I would have to go with latin names, latin is just awesome

Sol Invictus ( The Unconquerd Sun)
Terra Invicta (Unconquerd Earth)
Para Bellum (For War)
Mars Invictus (unconquerd Mars)
Vindicat Se De Vasari (Revenge upon the Vasari)
Divinus Pestis (Divine Pestilence)
Ira Sanctus (Holy Wrath)
Occidio Sanctus (Holy Slaughter)
Macellarius Sanctus (Holy Butcher)
Minerva Invicta ( Minerva the invincible) Feminin
Juno Invicta

Greek too

In Greek:
Hagia Sophia (Holy Wisdom)
Hagia Mania (Holy Fury)
Hagia Spathatos (Holy Sword Bearer)

I dunno why, but my advent flagship always ends up the Lux Aeterna (eternal light). something about their culture/unity makes this seem very appropriate.

also, the Para Bellum might not be the greatest choice seeing as the real life parabellum is a 9 mm bullet which is notorious for its cramped crew quaters

I normally pick a random name, such as;
Windexglow I
Windexglow II
Windexglow III
Windexglow IIV

And so on. Easier on the enemy to remember it's arch enemy

I don't have Sins yet but I have played GalCiv2 into the ground. Also I'm a great fan of US naval history so when naming my ships I tend to stick with US naval names so basically states, cities, people, and occasionally famous battles. However I always translate it world wide when in space so states = countries, cities = capitols, people = Great leaders, generals, inventors, philosophers, and famous battles just gets a much longer list.

Well if Im going to sacrifice the ship then Kenny

Main Battle Ship
Memor Morior = Remember to Die
Exspectata Nex = Welcome Death
Velox Nex = Quick Death
Terminus of Totus = End of All
Vita Terminus = Life's End
Purgo of Universitas = Cleanser of Worlds

Carriers
Plures nex = Many Deaths
Effervo = Swarm
Parum Vesica = Little Blades
Legion

I tend to go with my own fiction names that I've picked up here or there unless i'm feeling lazy in which case I drop UES in front of the ship's name.

Flagship
UES Explorer

Battleships
UES Pacifica
UES Righteous
UES Foxtrot

Carriers
UES Kyushu
UES Saratoga
UES Melbourne

Support
UES Erstwhile
UES Apex
UES Defender

i know this is most likely going to come with insults but when you name your ship does the name actually show on the hull of the ship your naming? if not that would be a cool mod id like to see. also if there was a tool that could let you customize the look of your ships.
but names for me are Excalibur, Romavictor, Thor, Achilles, Wallace, Ajax, Satan's Dragoon, Delightful Death, Odyseus, Neptune, Horus, Osiris, Anubis, Sphinx, Pyre's Edge, Guy Fawkes and a few more i want to keep to myself.
If u like these use em, no biggie to me

The "Cor Blimey" and S/S Jellied Eel are also good names

I use P words:

Perseverance
Persistence
Piety
Protection
Perfection
Pertinent
Persuasive
Perpetual
Prudential
Purity
Pursuant
Persecution
Petulant
Politick
Portent
Prodigy
Potential
Powerful
Predator
Premier

No prefix though, some of those words fill the available character limit by themselves.

One of the carriers in my expeditionary fleet always gets named after the TCS Tiger's Claw.