I'm still a bit on the newb side of things, but heres how I run things.
My first priority are the siege ships. Normaly, I'll detatch my LFs and send them after the siege frigs on their own. If that's not enough, the fighters lend a hand. But if I can't save the planet, or don't care about it, I'll just ignore the SFs.
As for chosing particular targets, I go mostly by ship types. The HC's I mostly leave to the AI to control. The LF's do a loop around the area and target support ships, starting with repair ships, then the Carriers, then whatevers left over (run 'em back to my repair ships when they get too damaged). The LRF's are what I run through the queued focus fire bit. Personaly, I start them off on the LF's to protect my support ships, then que through the HC's and other LRF's. Of course I break their que a lot, mostly to pick off the more damaged ships.
And the starbase? If i can ignore it, I will, and just come back for it later. If not, I generaly leave it to the Anti-structure cruisers and just use my fleet to defend them.
And bombers... They always start out on the jump inhibitors. Then the repair bays... then the weaker bits of the fleet.
Meh, thats my meager advice. This is how I do it against the AI. Probably won't fare to well on-line.
