Is there a good summary somewhere of what should go in each of the main folders in a linux install?

Solution 1:

Each distro may have their own quirks, but the overall file system structure should be more or less the same:

• "Linux File Structure" is a good overview of the directory structure.
• "Linux's directory structure" is a bit more verbose and goes into more detail about their contents.

Solution 2:

If you're installing X or Y, and it's not a standard OS package, then stuff should end up in /usr/local/bin, /usr/local/lib/, etc.

The Filesystem Hierarchy Standard and Linux Standard Base is probably a good place to start if you want to reference the closest thing there is to a standard list.