Hard to pick a favourite, perhaps One Size Fits All . Or "Shut up and play your Guitar". Or some of his more ambitious compositions like Yellow Shark. Or...
(I tend to prefer his middle period, when he had really proficient musicians and worked them hard, but before he ran out of steam - Broadway The Hard Way an unfortunate example of this. So the bands with George Duke, Patrick O'Hearn, Terry Bozio, Ray White, Ike Willis, etc. ) I'm a bit less keen on some of the early Mothers stuff, although it seems to be the musical basis for much of the good stuff that followed.
Other albums: Live in NY, Apostrophe, and of course the wonderful Hot Rats.