Mac only: In most cases, OS X does a good job of keeping permissions straight, but every once in a while things get messed up. If letting OS X repair them doesn't work, you can fix them yourself with free app BatChmod.
In most cases, when your permissions get out of whack, you can repair them automatically in Disk Utility. However, if you've copied a bunch of files from another Mac's home folder, for example, OS X may not understand what you want those permissions to be — only what they "should" be — and thus Disk Utility is of no use. You can manually edit permissions in Finder too, using the Get Info window, but you can only do that on a folder-by-folder and file-by-file basis — which would take forever.
If you're not comfortable changing permissions with the command line (which can be confusing even for those familiar with Terminal), BatChmod puts a great GUI behind the process. Just fire it up, pick the folder you want to edit and select the permissions you want to apply. With the click of a button, all your permissions will work the way you want them to.
BatChmod is a free download, Mac OS X only.