My Documents/My Games/FasterThanLight
If you can't find your Library folder, it's because on Mac OS Lion it's defaulted to hidden. Open a Terminal and enter:
chflags nohidden ~/Library/
Or just open Finder and "Go->Go to Folder" and enter the path
For most users, it will be in ~/.local/share/FasterThanLight/
...but if you modified XDG_DATA_HOME it will be in [XDG_DATA_HOME]/FasterThanLight
This was on the FTL website but putting it here in case no one goes to it.