Now that I have my PS3 pad working, I'll give a little input here.
The defaults I found okay, but I had to change a few things around. I use an xinput wrapper for my DS3, so the PC reads it as an XBOX pad.
First thing, I changed all movement over from the analog stick to the d-pad. The reason I have a DS3 is because it has the best d-pad of any controller I've ever used, compared to xbox d-pads, which are an abomination. I can understand why the analog is default in that case, but when you have a good d-pad, I find it works better since Valley takes digital input, rather than analog.
As a guy who loves his Megaman, Caslevania, and Metroid games, I should be able to press both Jump and Shoot at the same time with my right thumb. So jump gets moved down to the Cross button and interact to Circle. Primary attack gets moved to Square and Ammo attack gets moved to triangle, since it's the least accessible attack button. Secondary gets moved to L1 and Special to R1. Menu gets moved to the start button, since my fingers aren't on the sticks and it feels more natural for a guy who grew up with genesis/nintendo games. Also, Circle gets double duty as cancel and interact, since you use the confirm key instead of interact in menus, and don't use cancel while sidescrolling.
For reference, Cross = A, Circle = B, Square = X, Triangle = Y, L1 = LB, R1 = RB.