If you have not used Software Update in 4 years, you have a lot of updating to do. First do the following....
Disconnect all peripherals from your computer.
Boot from your install disc & run Repair Disk from the utility menu. To use the Install Mac OS X disc, insert the disc, and restart your computer while holding down the C key as it starts up.
Select your language.
Once on the desktop, select Utility in the menu bar.
Select Disk Utility.
Select the disk or volume in the list of disks and volumes, and then click First Aid.
Click Repair Disk.
Restart your computer when done.
Repair permissions after you reach the desktop-http://support.apple.com/kb/HT2963 and restart your computer.
From Software Update, install your updates 2 at a time and repair permissions. After all the updates are installed, restart your computer after the last permission repair.