Updated January 4, 2012
I was peeved at the lack of a checkpoint or game save function in FTL, so I wrote my own. For months, I've just been running it as a command-line script, but I thought I'd jazz it up and make it more Mac-shaped and release it to the public.
Although I've now bumped it to Version 2.0, I wouldn't be surprised if it doesn't run on somebody else's system yet, since, at it's core, it's a RubyCocoa app, and Ruby & XCode just love to not include things into a compiled package, where those things not included may or may not be present on somebody else's system. If you want it to work, and it doesn't, drop me a line and I'll figure out what to try and make XCode include in the package that doesn't come built-in to OSX.
OSX probably 10.5 or later
Your own copy of the game "FTL".
Launch FTL Checkpoint, then click "Play FTL." When you want to lock in a checkpoint, just choose "Save+Quit" in FTL, then immediately click "Play FTL" again. Now, if your ship is destroyed, if you just keep launching FTL with the "Play FTL" button, you'll keep restarting at your checkpoint. There's more in the help files included with the program.
This application is an original work by Dave Howell, and is copyright 2012. Others are welcome to download it, use it, make modifications, and adapt it, as long as appropriate credit/notice is retained. Please do not distribute this application without written permission from me. Distributing a link or pointer to this page is fine.
If you find this script useful or handy, all I ask is that you take the time to drop me an email at firstname.lastname@example.org and say so. Thanks. For that matter, if you find it not useful, that's an even better reason to drop me a line. I'll see what I can do to get to to work for you. :)