In a custom level
Edwards did this first (and maybe others have too), but he didn't document the process so I thought I'd do that for ya'll.
The custom level save is a file, and is stored alongside the "normal" save files. If you want to stop playing and still be able to resume later, you can make a copy of this file. It's located in ~/Library/Application Support/SketchFighter and named "Game 999".
In order to resume your save, you have to trick the game into loading it. Here's what you do:
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Load the map, find a save point, and save.
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Switch out of SF and replace the Game 999 file just created with your backed-up copy, giving it the appropriate name of course.
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Switch back to the game and commit suicide. Hit "Try Again" (return) and the game will happily load your previous save.
While this process may be something of a pain, the fact that it's possible gives me hope that custom levels may one day be blessed with a proper save system. My uninformed guess is that it was simply too large a feature for 1.0.1, because a new interface would have been necessary and this release was mostly about fixing bugs.