Hmmm...my favorites:

• Marza (TEC) -- Missile Barrage, Seige.
• Sova (TEC) -- Missile Platforms, Embargo
• Akkan (TEC) -- Colonization, Range Increase
• Progenitor (Advent) -- Colonization, Shield Restore, Cap Ship Resurrection
• Halcyon (Advent) -- Telekinetic Push, Extra Squadrons, Damage Increase Aura
• Evacuator (Vasari) -- Colonization, Nanite Attack, Phase Jump Inhibit, Planet Suck
• Devestator (Vasari) -- Seige Platforms
• Skinatra (Vasari) -- Scramble Bombers, Repair Nanites

Warning--in a game against real (human) opponents, you don't want to have too many capital ships because people will focus fire them to death and capital ships are really just support ships that can seige.  You'll get more firepower, overall, from long range frigates.  This is a very common mistake that new players often make.  (The AI in this game isn't real bright, which is why you can get away with having lots of capital ships against the AI.)

The Sova Carrier is by far, my favorite capital ship in the game. And favorite fictional spacecraft. I've been using it since day one, and loved it before the buff. The Akkan is also great to use by level six, and the Antorak Marauder is pretty fun to run.

My favorite capital ship?  I like the Egg (Vasari Evacuator mothership).  It is just so danged useful.  It can colonize.  It can help kill enemy capital ships and frigates with nanites.  The nanite ability also allows it to solo-colonize better than either of the other motherships.  It can trap enemy capital ships with its phase jump inhibit ability so that your fleet can kill them.  And then once it gets to Level 6, it has planet suck.

That would be the beta version of the TEC Kol Battleship. You can probably find a copy of the mesh floating around the Sins Modding forums somewhere (search it with the search function is a start).