FuSoYa's Lunar IPS is an amazing tool. If you're on Windows then go out and get that right now. Go go go! Unfortunately for us Mac users this isn't an option (unless you go get Wine or VirtualBox or some other Windows-in-Mac product out there).
For the rest of us -- and for only those of them who have Lua -- I wrote a short and simple Lua script to apply .ips patches to files. It was probably more a question of whether I could than of whether I should.