Contrary to popular belief, Disk Utility's Repair Permissions function can be very helpful. Here's an example:
Software Update wouldn't work (“There were errors bla-bla-bla). Installing from PKG gave a better error (checking from install log) something about broken DiscRecording Frameworks. Repair Permissions had this to say:
Symbolic link ./System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CFNetwork.framework/Versions/Current->A repaired Symbolic link ./System/Library/Frameworks/DVDPlayback.framework/Versions/Current->A repaired Symbolic link ./System/Library/Frameworks/DiscRecording.framework/DiscRecording->Versions/Current/DiscRecording repaired Symbolic link ./System/Library/Frameworks/DiscRecording.framework/Frameworks->Versions/Current/Frameworks repaired Symbolic link ./System/Library/Frameworks/DiscRecording.framework/Resources->Versions/Current/Resources repaired Symbolic link ./System/Library/Frameworks/DiscRecording.framework/Versions/A/Frameworks/DiscRecordingContent.framework/Versions/Current->A repaired Symbolic link ./System/Library/Frameworks/DiscRecording.framework/Versions/A/Frameworks/DiscRecordingEngine.framework/Versions/Current->A repaired Symbolic link ./System/Library/Frameworks/FWAUserLib.framework/Versions/Current->A repaired Symbolic link ./System/Library/PrivateFrameworks/Apple80211.framework/Versions/Current->A repaired Symbolic link ./System/Library/PrivateFrameworks/AppleVA.framework/Versions/Current->A repaired Symbolic link ./System/Library/PrivateFrameworks/BezelServices.framework/Versions/Current->A repaired Symbolic link ./System/Library/PrivateFrameworks/Bom.framework/Versions/Current->A repaired
After this and a 10.4.7 Combo Install, the machine worked fine again.
Another example, Activity Monitor wouldn't start, system.log had this to say:
2006-10-17 16:07:18.904 Activity Monitor The tool is not setuid root - please repair the privileges
Needless to say, repairing permissions fixed the problem. I've also seen cases where no application would launch - meaning you get the “blinking desktop” problem with the Finder constantly trying to start itself up. It was caused by a broken /tmp symlink (which in OS X links to /private/tmp, and we also have /var/tmp!) which Disk Utility nicely repaired.
Repair Permissions is often called the “PRAM zap of the 21'st century” and I agree. But just as a PRAM zap could fix a no-video issue, Repair Permissions can also help sometimes.