C is for command-line stuff. L is for handlers and filesystems. S is for scripts. The difference between Tools and Utilities is so vague that they've been consolidated in OS4.0. I put small applications in Utilities (media players, text editors) and generally leave Tools alone. Commodities is, not surprisingly, for commodities (readme files should tell you if a given program is a commodity). I usually don't touch System.
The Workbench and DOS manuals probably document this, too. I'm not sure. Technically, you can put anything anywhere you want, just as long as you know how to access it when you need it.
