Hm, depends a lot on what you're building for.
Generally-speaking, I'd go for Target Analysis, Reliability Engineering, and either Gunnery Implants or Energy Weapon Mastery as being the must-have options.
Point Defense is really good, but you can't get both it and Target Analysis (unless you have Officer Training), so... go for PD if and only if you're setting up an officer for an escort vessel, something that isn't meant to actually contribute to killing cruisers or capital ships.
After those, season to taste. Ranged Specialization is good for capital ships and some cruisers - but locks out Impact Mitigation, which is also really good for those same low-tech ships that really want Ranged Spec. Shield Modulation is really good for, well, anything that's not phasing or cheesing derelict contingent. Systems Expertise and Missile Spec are very ship-specific; depending on what you have in your fleet they can vary from really strong to virtually useless.
Helmsmanship is decent but not a must-have, though it does benefit from having one of the better elite options.
And, last but not least, keep in mind that officers level really fast. As long as you haven't burned a story point on eliting one of their skills, feel free to fire and replace them if their skill set no longer matches what you're fielding.
