@Dominus
For the Metroid games where you need to keep pressing the Select button or like Wrecking Crew on the NES where it kicks you out of the current game when pressing Select, I made a config file with the same name as the rom with .cfg appended to it (like Metroid.zip.cfg) and then setup the Guide/Logo button as Hotkey on my Xbox 360 controller just for those games:
Or you can change it for every game on 1 system (like for MAME2003) by added the above to this file:
/opt/retropie/configs/mame-libretro/retroarch.cfg