That could be done probably through epsxecutor or delta frontends. The problem lies in the lack of support for pad plugins. Whenever that feature kicks in, i bet you'll have the possibility to have a different control set for every game. I know they were working on it for 1.6.0, but a data loss prevented it's appearance in the release. Hopefully it will be in a future release, but please don't ask when will that be. We honestly don't know. It's out when it's out .
Well less of the probably and more of the already .
Both frontends already support pad configurations. Although that said epsxecutor does it's keymapping via epsxe itself, so most folks could be excused for not realising it even existed (hell I wouldn't have known it was there except for the fact that I analysed it's registry keys when writing my file converter ). Also, for the reasons I-Chan stated epsxecutor already has pad plugin support, even if epsxe doesn't .
As for Delta, it uses it's own configuration dialog for that, but there's a bug regarding psx pad converters on the current release (Damn you lot for only pluging 1 pad into those things when they always expect to find 2 ). Theres a beta on the forum somewhere with the fix, if you want to go hunting .