Captain skills retrain
I wrote a guide about just this topic with links to resources to figure this out (the link to ryansto's video is particularly good for DPS).
http://fleet.stonewallgaming.net/forums/guides-and-walkthroughs/74818-how-to-use-skill-points
On my toons that are set for space dps, I max out attack patterns, energy weapons, energy weapon specialization, weapons training, warp core efficiency, electro-plasma systems, flow capacitors (for leech), and particle generators (if you're using science damage-inflicting skills).
Also, for survivability and dps, maneuvers, targeting systems, structural integrity, armor reinforcements, impulse thrusters, warp core potential, hull repair, shield emitters, and shield systems are all worth 3 to 9 points depending on what you're doing exactly.
And this isn't to say that the other skills are useless, but it depends more on the rest of your build. The 4 engineering skills that give a bonus to a subsystem are all pretty valuable if you don't have too many other bonuses to subsystem power.
http://fleet.stonewallgaming.net/forums/guides-and-walkthroughs/74818-how-to-use-skill-points
On my toons that are set for space dps, I max out attack patterns, energy weapons, energy weapon specialization, weapons training, warp core efficiency, electro-plasma systems, flow capacitors (for leech), and particle generators (if you're using science damage-inflicting skills).
Also, for survivability and dps, maneuvers, targeting systems, structural integrity, armor reinforcements, impulse thrusters, warp core potential, hull repair, shield emitters, and shield systems are all worth 3 to 9 points depending on what you're doing exactly.
And this isn't to say that the other skills are useless, but it depends more on the rest of your build. The 4 engineering skills that give a bonus to a subsystem are all pretty valuable if you don't have too many other bonuses to subsystem power.