There was a Lua[JIT] fork called Idle that seems to have fallen off the face of the Earth that did exactly that: it would take a small stub program, a runtime library and all the scripts and package them into a single PE/COFF binary that would read itself when run.
Love2D does it as well:
zip -9 -r SuperGame.love .
cat love.exe SuperGame.love > SuperGame.exe
This doesn't work with ELF files, though.