Definitely thumb and three fingers for me - my middle and ring fingers are pretty much interchangeable these days, and seem to decide between themselves who's picking up the work as it comes in

Doc's another one who picks with just thumb and index, and I'm always in awe of that - but then look at what he can do with a single flatpick...
As for resting a digit or more on the top of guitar, I think I used to do that, but if I try it now my hand feels as though it's in a straitjacket. I think some of it's down to muscle memory and some down to the guitar you play - I'm currently using an F-sized Lowden and that body size seems to drop my wrist and hand just where they need to be.
By complete coincidence I was watching Pete Huttlinger's (excellent - they all are) Essential Exercises for Fingerstyle Guitar yesterday and he mentions this very issue. His take is that the soundboard is the major element in producing the guitar's voice, and that resting one (or more) fingers on it will have an adverse effect on both volume and tone.
It's also frowned up by classical guitarists, although I suppose much of what we do is. I've been watching, listening to and trying (with varying degrees of abject failure) to play a lot of Leo Kottke lately and his right hand is a study in itself. He went back to basics after near career-ending tendonitis, and now picks with his (pickless) thumb well forward and his fingers almost perpendicular to the strings - quite apart from the relentless movement of the hand, that position renders it all but impossible to rest anything on the top of the guitar.
Thankfully there is no 'right' way - we find the way that works for us, and for the lucky few, those breaks of the 'rules' can be the thing that marks them out from the crowd.
Happy picking
