Can I reset everything to its factory default settings?

You can restore gnome-specific settings with the following commands in terminal:

rm -rf .gnome .gnome2 .gconf .gconfd .metacity

For details you can see How to Reset Ubuntu/Gnome Settings to Defaults without Re-installing | Linux FUD

Additionally you can verify that there are no broken dependencies using:

sudo apt-get check

And then you can troubleshoot your remaining problems one-by-one.

What I would suggest is to backup important files, insert the installation disc (or usb) then reinstall ubuntu. It will give you the option to wipe/install over the previous version. Then use nepomuk to make a backup after you've got everything installed.Make sure that you only backup things you need like your home folder and try to backup (i think) your ppa list

It is a hard job.
But I have manage to avoid the hard job through an unusal way.

1 , create a new account , for example , mark

 adduser mark 

2 , mv your personal files to home directory of mark's

 mv yourfile   /home/mark/  

3 , change the ownship of your file to mark

 chown  -r yourfle   mark

3, logout , and then login as mark

4, GNU/LINUX will allocate mark a new home directory as well as a default system environment . And everything is ok now.

5 , Be careful , you have to get the root permission to do so .