V.A.T.S Hit 'em in the...

[kouriichi]

I hit em where it hits.
If i have a 70% chance at the chest, and 20% at the head, im putting a few rounds in his center of mass.

So my answer, where ever i have the highest percentage.

 

[DannyJBeckett]

In Fallout 3:

Humans: Head
Super Mutants: Arms, because it'll make their aim even worse
Super Mutant Behemoths: OH GOD SHOOT! JUST SHOOT IT!
Centaurs: Head and tongues
Radscorpions: Stinger or legs
Deathclaws: Legs
Ghouls: Head, same as humans
Sentrybots: Head or the arm that shoots missiles
Mr. Gutsys: Eye-stalks
Robobrains: erm.. Brains
Protectrons: Head
Mirelurks: The face, if you can. If not, the legs
Mirelurk Kings: Head
Ants: Antennae & head
Yao Guai: Head or forelegs
Dogs: Head
Brahmin: Heads
Mole Rats: Head
Bloatflies & Radroaches: Anywhere!

Extra creatures in New Vegas:

Cazadores: See behemoth description
Coyotes: Head, same as dogs
Geckos: Head
Night Stalkers: Head
Spore Plants: Anywhere
Bighorners: Head
Giant Rats: Anywhere