Care to share which software you updated?
You can still update your Apple apps by going to the Download website.
Regarding SU, try the following: HOME>Library>Preferencs. Trash the com.apple.SoftwareUpdate file.
Disconnect all devices from the computer then do the following:
Boot up from your Snow Leopard Install DVD while holding down the "c" key.
Select the language you wish to use, and then choose "Disk Utility" from the menu bar.
Your HD should appear in a panel on the left hand side of the window which opens. Select it and then click on the "repair disk" button in the right hand section of the window.
Once this process has been completed restart your computer and repair permissions directly from Disk Utility. Empty the trash. Plist file will be recreated the next time you open SU.
If Disk Utility is unable to complete the repair, you will need to use a stronger 3rd party utility like DiskWarrior, Techtool PRO (not Deluxe) or Drive Genius.