Couple more notes: As I have started to do some backing up (manually since time machine needs to be accessed through the system preferences) I have noticed that there are a few files that will not copy since the mac thinks that they are 'in use.' A movie, a photo, etc. I have tried to open iPhoto to see if I can open the image in question so I can close it properly. When I did this, iPhoto crashed. It seems that when I scroll through the library, it seems that when I get to a particular file, it crashes.
I have also noticed that my speakers have stopped working.
Could all of these, combined with the initial problem of not being able to open the system preferences, point to a larger issue?