Just from personal observation:
Perks that work (or at least seem to, from what the game tells us):
+Hitpoint perks in the melee & medicine trees
Melee weapon speed/damage perks
Smithy refining perks (efficient charcoal, making steel, etc)
Disciplinarian perk in Leadership (only after they patched it to work after enough folks yelled about it)
And, okay, there's probably a couple others that function and I'm just not thinking of them right now.
Perks that either clearly don't work, or it's hard to tell if they work or not because they're so insignificant or RNG-dependent, or we have no idea because they're high enough in a skill tree that the leveling system is never going to let us even try them:
Pretty much everything else
Perks where it doesn't matter if they work or not, no matter how good they are, because we're simply never going to use them, probably not even with companions:
All perks labelled "Governor"