I forget the encounter name, but there is a general patrol encounter that ALL factions use around major facilities. I inserted capital ships into this patrol encounter. Now whenever I am around a military base or jumpgate, cruisers, gunboats, and destroyers will all jump in and out of the area. Its the easiest way to add cap ships in game without editing every single encounter file. Also, I gave several factions of pirates a "captured luxury liner" as a capital ship. This also was inserted into the patrol encounter. I now have pirate luxury liners flying around pirate bases.
To add a little capital ship battle excitement, I created a pirate capital ship encounter using the luxury liner pirate ship. It will randomly spawn a pirate luxury liner along with 2 or 3 fighters into a military area that is heavily guarded (usually by a military battleship) The fight that ensues is quite fun to watch, although if there is a battleship in the system, the pirate cap ship usually gets toasted pretty quick.
I also created a bounty hunter assault encounter. It basically adds a bounty hunter armored transport to bounty hunter patrols that fly in areas around pirate bases. It adds a little excitement when visiting your favorite villians.
When I get home, I will post up my custom encounters I made. Tweaks will have to be made to make the ships run if damaged though....