Actually quite a few use the select button to do things like ship speed in certain shooters, and inventory screens in others. So in that regard, the Ave3 pad comes in really handy, as the "third" button can be set to act as either Select or Run.
As for 6B support, I know Martial Champions and Strip Fighter 2 both support it, (although MC is only 3 buttons).
A full list of 3 & 6B supported game would be nice...