Basically you want to kill the most dangerous targets first. However Range and Fleet type matter a lot here. If you're fighting short range don't call that bs that's 60km away primary. You might want to split firepower between short and long range targets if you have a mixed fleet and the enemy is also fighting at mixed ranges. If you are preforming hit and runs your support should make enemy tacklers primary.
It's almost always best to call primaries alphabetically or reverse-alphabetically. The predictability helps your tacklers get points and your battleships to lock shit up in advance, and can make a huge difference.
See Common PvP Ships for a list of common ships sorted by role.
- Electronic Warfare ships (Scorpions, Blackbirds, Celestis, Recons, some Ravens/Ferox)
- Enemy fleet commanders (if they are not tanked out)
- Covert ops
- Logistics ships
- Dps/Sniper Battleships/Hacs
- Tanked battleships/Battlecruisers