Killing them. For 2 reasons:
- The possibilities are endless! I've killed some in very unique ways. You can also get some of them to kill others. It's quite sadsitic! :P On the other hand, there's usually only one way to save a single Mudokons.
- It is, in fact, much harder than saving them. There are some puzzles that include Mudokons that are quite easy to save, but the developers didn't design them to allow the player to kill the Mudokons, which creates an unintentional (yet fun and challenging) puzzle, in which you have to use tricks involving the AI system, passing areas designed to require a Shrykul without using it, and so on.
My "worst" record: (Today I'll start a new game, trying for even worse!

)
276 killed
8 saved (6 from the early levels, 2 from the game ender)
My best is perfect (300 saved)