I'll just be covering the ships seen in HQ sites and using the shortened names. Look elsewhere for more details/lore. Ships are listed roughly order of what to shoot first, within each class.
Battleships
Outuni - Devastasting energy neutralizers, also scram and webs. Seen in all three sites. Usually highest priority.
Deltole - Moderate energy neutralizers. Also scrams and target paints.
Intaki - Remote reps, usually killed early on
Ostingele (Osti) - Generally DPS fodder
Yulai - Generally sniper fodder.
Cruiser
Arnon - Can jam multiple ships. Kill immediately.
Vylade - Boosting ship. Generally killed early on.
Mara - Remote repping ships. Usually killed early on, and usually by snipers
Antem - Cannon fodder
Auga - Scrams and webs
Romi - Cannon fodder.
Frigate - Frigates are usually only killed by the DDD. If you are DDD, kill the Niarja first, then use the acronym moNSTER to remember the order.
Niarja - Jams and energy neuts. Kill immediately.
Schmaeel - Scram and webs.
Tama - High alpha stealth bomber
Eyster - Cannon fodder
Renyn - Webs. Cannon fodder
Battleships
Outuni - Devastasting energy neutralizers, also scram and webs. Seen in all three sites. Usually highest priority.
Deltole - Moderate energy neutralizers. Also scrams and target paints.
Intaki - Remote reps, usually killed early on
Ostingele (Osti) - Generally DPS fodder
Yulai - Generally sniper fodder.
Cruiser
Arnon - Can jam multiple ships. Kill immediately.
Vylade - Boosting ship. Generally killed early on.
Mara - Remote repping ships. Usually killed early on, and usually by snipers
Antem - Cannon fodder
Auga - Scrams and webs
Romi - Cannon fodder.
Frigate - Frigates are usually only killed by the DDD. If you are DDD, kill the Niarja first, then use the acronym moNSTER to remember the order.
Niarja - Jams and energy neuts. Kill immediately.
Schmaeel - Scram and webs.
Tama - High alpha stealth bomber
Eyster - Cannon fodder
Renyn - Webs. Cannon fodder