Picking the right equipment for your ship at level 50 is a huge topic, and often it doesn't just involve picking the equipment but also involves what bridge officer skills you use in space combat. Before I go into the deep end, lets start with something simple:
The Beginner's Set
The set consists of 4 items that are relatively easy to obtain and is one of the most defensive setup in the game:
The MACO shield is one of the best in the game (and much, much, MUCH better than the Borg shield). The 3-piece Borg set unlocks the Borg set's additional powers. It grants a 2% chance to repair your hull and a 20% chance to restore your shields every time your ship is damaged.
Bridge Officer (BOff) Abilities
As you get more experienced with ship combat you should start relying more on your BOff abilities to keep your ship from exploding and rely less on your ship's gear. The good defensive BOff abilities include Emergency Power to Shields, Tactical/Engineering/Science Teams, Hazard Emitters, Transfer Shield Strength and Polarize Hull. Make sure you have at least 3 (I typically have 5-6) or more of these abilities and use them regularly to keep your ship in good condition.
When you have a good grasp of your BOff abilities and can reliably use them to keep your ship in good condition, that is when you can start weaning off from the Borg & MACO set.
The other equipment sets tend to offer less defense but in exchange gives your ship more offensive capabilities. For example my current favorite is the Omega Set. When used with high rate of fire weapons such as cannons and turrets, the Omega Set's Tetryon Glider and Gravitic Anchor powers allow you to quickly remove an opponent's shields and cause a lot more hull damage.