Or, ensure that they're not system-level or Mac OS X-specific folders (in other words, they are folders you created), and just set the permissions on the folders to exclude users who shouldn't be perusing them.
Eh - not quite...
OS X user accounts are admin by default.
An admin account lets you do a lot of things, but NOT "anything you can".
That access level is reserved for the superuser, or the root user account (which is NOT enabled by default, as that level leaves your Mac wide open)
I almost forgot about the 'chflags hidden' command until i remembered the article Hide Folders in Mac OS X. You can modify that command to use it when you ssh into each Mac.
Good luck and be careful and remember where you hidden the folders.
The first is to put a period in front of the name of a file or folder. That makes it invisible. There are some nice free utilities that will allow you to make invisible files visible, so this is only a very basic level of protection.
If you want a very high level of protection you can create an encrypted disk image using Apple's Disk Utility (part of OS X) and put any file or folder in the disk image and password protect it. Not even the FBI would be able to open an encrypted disk image.
I can give you the instructions for creating an encrypted disk image or an invisible file using tools included with OS X, but the following free utility makes things so easy, you will probably just want to go with it: