RetroArch currently supports UPS, IPS and BPS patching formats. If you load rom.bin and one of the following is present, the ROM will be autopatched: rom.ups, rom.ips or rom.bps. Autopatching only takes place if the libretro implementation supports loading ROMs from memory.
You can apply multiple patches to one ROM by naming the patches with the .ips$ extension, where $ is a number. For example, given the following files...
rom.bin
rom.ips
rom.ips1
rom.ips2
...rom.bin will have rom.ips, rom.ips1, and rom.ips2 applied to it in that order.