Safari, Limeiwre and Software Update won't open

Ok, my sister just called me with a slight panic. She said that she was doing Software Update, and during the Update, her computer froze, so she was forced to just power it off. When she turned it back on, the programs that were running at the time, Safari, Limewire and the Software Update won't open. She said that they icons bounce on the dock a couple of times, then just stop. I gave her some suggestions like zapping the PRAM, Repairing Permissions, and we were going to try to Rebuild the Desktop too, but it wouldn't do anything. Also, her iPod won't show up on the Desktop or in iTunes now for some reason. It will charge, but it won't mount.

Any Suggestions?!