Humans: all humans in the wasteland came from a vault at one point or another, or are the offspring of vault dwellers
Ghouls: humans who survived the Fallout (no pun intended) and where not in a vault. The substantial radiation changed them, and most ghouls are actually 200 or more years old.
West Coast Super Mutants: Enclave experiment late taken over by Richard Grey, aka "the master" and ripe individuals were plucked from the wasteland and dipped in FEV
East Coast Super Mutants: Pretty much same as above...only on the east coast.
I guess what confuses me are little inconsistencies, like Shady Sands in F1. Those folks came from Vault 15 right? So how come Tony Shalhoub is skeptical when you tell him you came from a different vault?
I hope these questions make sense. Thanks for any replies!