It depends on if you enjoy V.A.T.S or not. If you're planning on using vats, then Action Boy, Grim Reaper's Sprint, Sniper, Concentrated Fire, Ain't Like That Now, Commando, Nerves of Steel, and a few others are all good.
If you don't care about V.A.T.S, then demolition expert is one you definitely want to max for explosives (I think it's 3 points). Trigger Discipline is a good trait to pick up, as well as Skilled. You want to take a lot of the damage perks such as Purifier, Robotics Expert, Confirmed Bachelor, Lady Killer, Bloody Mess, Living Anatomy, and Hunter. (Certified Tech helps against robots, but you get it at a higher level). As for choosing the level 50 perk, it's split between more action points, no taking critical hits and 20% faster shooting (Bad Karma version), or 10% damage, a TON of health if you are a good karma character, and no taking critical hits (Good Karma Version). (I honestly think that the Neutral Perk at 50 is really crappy).
Jury Rigging is also a pretty good idea if you can get to it. After that, it's going to be mainly preference. (I can't stand playing without Rapid Reload, though, so I normally pick that up as quick as I can.)