Every d20 game has things I really, really like combined with varying degrees of things I really, really hate. I also just don't have the time or energy to find that mythical perfect RPG anymore, so I'd rather hot rod the d20 chassis with the plethora of diverse published rules floating around out there. From that perspective, I actually kinda like the idea of not having a favorite implementation. Still, here's a few notables:
From the few times I've actually been able to run it, Pathfinder works really well. Too well, in fact. I don't feel like I can open up the hood and poke around without causing serious damage to other parts of the system. Vanilla Pathfinder does make for some nice Vanilla Pathfinder though.
Mutants and Masterminds feels a little the same way in that I have a thousand by-the-book options to tinker with it, but I don't feel like I can eyeball anything. It also makes me buy into a lot of options that make good sense but just aren't as fun for me, like wound rolls, or weird, almost contrary alternatives.
I really, really like a lot of what Fantasycraft has to offer with characters on both sides of the table and gm design mechanics, but I can barely make sense of it while flipping back and forth through the book just to look up the rules on a few core concepts.
I like how BESM d20 is slim and already broken enough that I don't have to worry about ruining it any more when I tinker with it. I'd kinda like to run Pathfinder on the BESM core without all the trait options.
Action! has a lot of cool things going on, but it's a skeleton of a system that's so alien to any other d20 game, that I don't think I could ever squeeze out much of any great substance that other games like M&M hasn't salvaged from it and combined with rules that aren't quite as charming. Action! is a real heartbreaker.