MRC user Popolon_fr started a discussion about customizing games to be played with a SNES joypad about a month ago. To connect such a joypad to your MSX you first need an adapter of which you can read all you want in its wiki.
This newspost gets an update once in a while as Popolon_fr keeps on releasing patches.

Yesterday he uploaded the following JoySNES patches he has been making in that month:
Metal Gear
Metal Gear 2 - Solid Snake
Maze of Galious
Hinotori aka Firebird
The Treasure of Usas
King's Valley II