Turns out GCC 3.x support -isystem also, they just don't document it.
[pintos-anon] / src / utils /
drwxr-xr-x   ..
-rwxr-xr-x 1820 backtrace
-rwxr-xr-x 3695 checkbochs-trace
-rwxr-xr-x 21921 pintos
-rwxr-xr-x 975 pintos-mkdisk