If, for whatever reason, you (or the reason) delete vital symbolic links (such as /var, /etc, /Library/ColorSync/Scripts, etc.), you can restore them using a Permissions Repair. After running the GNU cleanlinks utility (thankfully not as root!), I found that it had deleted over half of my system's vital links (and tried to delete the other half, but fortunately ran into a 'permission denied' problem).
I opened Disk Utility, selected my main hard drive and clicked the 'Repair Disk Permissions' button, and Disk Utility ran through setting up symbolic links for everything again:
Contents/Frameworks/GLResourceViewer.framework/Resources repaired
Symbolic link ./Developer/Applications/Graphics Tools/OpenGL
Profiler.app/Contents/Frameworks/GLResourceViewer.framework/Versions/Current repaired
Symbolic link ./Library/ColorSync/Scripts repaired
etc.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20040610153708159