What's your style of aiming?
Usually, for the LMG, I try to strafe past the skulk or back away from the skulk as I aim. With the pistol, it's just point and shoot.
With the shotgun, though, I tend to get very twitchy. In fact, I tend to miss a lot more if I'm not reacting. I just can't seem to aim as well when I try to aim ahead. When I have a shotgun, I usually see the alien come and maybe plan out when I'm going to shoot. Usually, though, I see a skulk marching along the floor and I jerk my mouse down to shoot it. Same with lerks. I can actually hit a lot of lower lifeforms this way, for some reason, and can manage a full 180-degrees spin to hit a skulk behind me if I get scared. A drawback to this is that I end up clipping my teammates with a couple of the outer pellets occasionally.
With the knife, I used to just hold down +attack and come out swinging, but I find that it's only useful to intimidate a skulk. Once I get down to the actual shanking, I try to jump around and swing upwards, if I can, swinging only when I want to hit. If the skulk goes for my head, then I just swing at his belly, clicking only when I plan to attack.