In my science ship I rely on gravity well and EWP for my damage, so I always prioritize the slowest movers -- I might switch over to an escort and hit him with SNB if I see the rest of the team firing on him, but I can't usually damage an escort since they usually just zip away without even trying. Healers are usually very easy targets for that ship.
In an escort, I usually pick a carrier on the first pass if I see one. Better to kill them before the get pets out. If they turn out to be squishy, then I'll keep coming back to them whenever they show up
DPS cruisers are my next pick (Tacs preferred, but any cruiser that trades high level engineering offensive powers for the defensive/healing ones is likely to be squishy). It's easy to just sit and burn down one shield facing on a cruiser, and there's nothing he can do to get away, so they're usually first.
After that, Science ships of any type, though if they turn out to be tanky I might pass. Still, even the tanky ones have frail hulls, so all it takes is their shields dropping for a split second.
Escorts are a "sometimes" target. My general philosophy is to take the most firepower from he enemy with the least effort, so if I notice a particularly squishy escort then he'll be my first target every time. But they are generally the most difficult targets (healers and well-played cruisers or carriers seem worse, but there seems to be more of a divide there. Any escort that binds EPtS to the space-bar and runs a few copies of APO is going to be relatively tough without requiring much skill)
If I'm feeling silly and DPSing in a cruiser, then carriers are my #1 target. I basically sit on top of them with EWP and FAW to remove them and their freaking spam from the game until eventually they pop. I can't say its all that efficient, because I basically give up any other meaningful contribution to create a no-fly zone, but I really hate pets. If 2 or 3 carriers are close enough to support one another, I can usually keep most of them and their pets locked down.