ebootFIX.exe

This tool processes whole game folders;
drag & drop the folder of whatever PS3 game, the parent
folder holding all the game files and sub-folders onto
this executable and after it crunches away
you’ll be left with two new folders: [NPDRM] and [RETAIL].
What’s the diff? From _readme.txt:
[NPDRM] – content ready to be installed as PSN-style XMB game:
You will find two PKG files in the folder.
The tool will decrypt and sign all executables (EBOOT.BIN and
other .self / .sprx files) to make them compatible with lower firmware versions.
Follow the generated INSTRUCTIONS in [NPDRM] folder.
[RETAIL] – all files which you can replace in your original backup copy to play the
game via a Game Manager.

ebootMOD.exe

This one takes a single file — drag & drop an
EBOOT.BIN or a .self or .sprx — and it’ll result in a
decrypted and signed file that is again
compatible with lower firmware versions.
Of course you can find more info in “_readme.txt” and at the source.
Also included is a version of multiMAN v1.16.11;
a test build that properly handles sprx files when using “shadow copy.”