Despite John Gruber's longstanding assertion that "Repair Disk Permissions is voodoo," Brian Tanaka has published "Take Control of Permissions in Leopard" for the Take Control series of eBooks. It's part troubleshooting (how to delete stuck files, for example), part tips and tricks (the best ways to keep files private) and part theory. It's only $10US for 87 pages of very useful information.
For example, you might learn that repairing permissions with Disk Utility won't change the permissions to any of your user-centric files -- it's meant to restore [Apple's] application and system file
preferences permissions to their as-delivered condition. Even if you do think that Repair Permissions is nonsense, it'll be nonsense you fully understand.
[Update: John Welch pointed out the typo in the 2nd paragraph; of course, Repair Permissions changes permissions, not preferences.]