I have always been a fan of assault rifles. I don't why I tend to gravitate towards the, but I just do. For that reason, I took a quick liking to the Commando for his proficiency with assault rifles, his ability to see cloaked enemies, and his ability to see enemy health bars.
Though he was a real pain to level up (why do I need to kill stalkers? A commando's only relationship to them is that he can see them.), it was the perk I maxed out (and, so far, the only one).
My second favorite perk would have to be the Medic. I enjoy just sitting back and keeping the team in tip top shape (health-wise) while dealing with the lesser threats. I also enjoy running around like berserker and trying to salvage a game when the rest of the team has died (shame that that's coming to an end with the re-balancing),even though I usually fail and get a game over.
Third is Sharpshooter. I love being able to pull off Headshot kills with (relative) ease compared to the other perks and doing it with a handcannon (or dual handcannons).