For me most of the VATS perks are completely useless. I have a mouse and a keyboard, VATS feels clunky and out of place. It's, to me, nothing more than an "Oh shit!" handle, something I use when I'm overwhelmed and seldom beyond that. So anything that affects AP costs, VATS accuracy and the like is ignored outright.
Perks I almost always take:
Tag!(Free 15 skill points, why the hell not?)
Animal Friend(Dealing with things like nightstalkers and wolves is just tedious. It doens't make the game any harder it just makes it annoying to roam the wastes)
Intense Training(I usually leave with a 10 Luck stat for purposes of clearing out the casinos with ease. This, of course, means the rest of my SPECIAL is meh. Taking a few ranks of this helps greatly, usually aimed at STR, END and INT.
Almost Perfect(Because why not?)
Confirmed Bachelor/Black Widow(Easy way to deal with Benny + 10% more damage against all humans in-game, no brainer really)
Silent Running(My monitor is dark and traps can be annoying, so I take this to avoid setting them off when I don't see them.)
Jury Rigging(Fix anything with anything? Hells yeah!)
Living Anatomy(Lets me get better sneak crits since I can see their DT/HP BEFORE I start a shitstorm and select the appropriate hardware)
Infiltrator(Lockpicking is a bit on the tedious side, too, so I like being able to hit F and get into most things)
Comp Whiz(Same basic idea, I can just randomly click terms and not get locked out, though since Nevada Skies borked that and terminals only spit out one term anyway it's kinda moot right now.)