I always wondered how thumby's managed to play Super Mario Bros games. I mean, do you like roll your sideways thumb back and forth to run and jump or do you guys just walk through button combo games? 
I normally use two fingers to play challenging games, so I can hold down the run button in SMB and then jump whenever I feel like it or time perfect head slams in Bonk without moving my thumb all over the pad.
But when I'm sleepy or lazy I just use my thumb.
You're referring to SMB / Adventure Island / Wonderboy 1 / JJ & Jeff platformers?

I should take a picture (maybe I will!), but the top-half of my thumb rests on the B / II button. Whenever I need to hit A/I, I use the middle of my thumb (where the crease is on the underside). It is incredibly comfortable and I don't find it awkward like the multi-finger method. Sometimes my thumb is nearly horizontal, but it shifts depending on the gameplay.
I love Wonderboy 1 & company, and now that I think about it, my method for holding the controller was borne from playing them.

Also: We've discussed our preferences for controllers in other threads, yet it never occurred to me that the manner in which we hold the controllers was such an important consideration.