All default Apple applications do not start/work and do not open! No Finder

Lately, I got some problems on my Mac Pro 10.5.8, and I thought it might have to do something with the operating system. So I tried to update the system with Pacifist (by choosing to replace all the old files; since by default it just update only if there is any version change). Well it turned out the problem was in hardware, which I resolved but now all the Apple software is not working; the rest all do. Which means, no Mail, iCal, address book, etc (iLife works though). What I see on the dock are just white icon with App logo on it. Even finder icon on the dock has vanished, although I can open finder by clicking anywhere on desktop, and then choosing it from menu.
Can someone please suggest what I need to do? Is it a permissions problem? (I tried repairing all permissions already, did not work!
Do I need to reinstall the whole OS? I wanna avoid that at this stage.

Try downloading and running the 10.5.8 combo updater:
http://support.apple.com/downloads/MacOS_X_10_5_8_ComboUpdate
Failing that, consider an Archive and Install:
http://support.apple.com/kb/HT1710
Good luck!

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