To do it:
Go to Applications->Utilities->Disk Utility.
In it, select the drive which hosts OS X (likely, your only drive) by clicking on its icon on the left-hand side. "Repair Permissions" should now be clickable - click on it.
What it does:
OS X is UNIX-based, and all UNIX files have permissions (essentially, read, write, and/or execute - run - for you, for people in your "group" and for everyone in general). If the permissions get messed up, then, for example, you wouldn't be able to run an applications because the "execute" permission wasn't set for you. Sometimes, permissions get screwy - often during major installs - and Repair Permissions makes sure it's all fine and dandy again.