It depends on play-style and mode. For example, alot of people will vouch for Small Frame, myself included. However, on hardcore broken limbs are more of an issue, and possibly more so if you go with melee or something like that. Built to Destroy is another alot of people like, as the advantage of 3 extra crit tends to outweigh the extra weapon degradation. This is especially true if you are good about making weapon repair kits or take the Jury Rigging Perk. All others seem to be more or less situational, if you got a question about a specific one your looking at lemme know, I'm sure myself or others on the board can give you a helpful impression.
Forgot to mention Four Eyes, as it deserves a special mention. It counts as having one LESS perception than you put into it when creating your character for the purposes of perk requirements. Unfortunately, perception, while not entirely useful on its own, is required for some pretty good perks. so alot of people would advise you to stay away from that one.
Bulit to destroy if you're into criticals, heavy-handed if not. Small frame if not playing hardcore, and kamikaze if you're into VATS. Wild wasteland as well for some comedic special encounters. --- Does this rag smell like chloroform to you?
I'd say the very best abilities are Built to Destroy for the extra Crit chance, and Good Natured. Good natured may seem odd, but since you can't really focus on more than one combat skill you really only lose 5 points while gaining a lot in other vital skills. --- I just shoot them in the face repeatedly. If I have a Winchester, and they have a face, I'll win.
The only drawback is the reduced accuracy, sure if you never use VATS, fast shot is the best trait you could pick. But for a critical expert, the increased DR and critical chance should not be ignored, also there are perks to using vats such as a very awesome one including the multiplas rifle, one roll to crit and 3x the critical damage boost. --- Does this rag smell like chloroform to you?
Fast Shot is a better VATs trait than Kamikazee because of the increased efficently of action points. The accuracy loss is not noticeably with high gun skill. Fast Shot only increases spread anyways IIRC.