I recently had a permissions problem on Ubuntu, caused by an aborted attempt at using Remastersys backup software which I don't think I will ever use again judging by the mess it created. Ha! to think I was using it to protect my sacred install!
It all meant I had to create a new user account and copy everything across. I did this once logged into the new user account. Annoyingly my other storage partitions (under /media) had to have their permissions changed aswell, I did this by loading konqueror as root (rather than using sudo konqueror as I've found that it wouldn't always change permissions underlying directories for some reason and was slow. It was still slow changing permissions on gigs of files.
Anyway, there was a silver lining to this story too. As i only copied important files and directories such as .evolution for my emails and .bash_history so i don't have to keep trying to remember obscure commands in terminals. Secondly I decided to start Firefox from fresh, well almost fresh, as it had become slow and bloated from many extensions and cache detritus etc. I used the FEBE extension to restore passwords and selected extensions from my old firefox. It runs a lot quicker now :)
My Favourite Firefox Extensions:
Foxmarks (for synchronising bookmarks between browsers)
Delicious Bookmarks (similar but more accessible)
Download Embedded (for vids)
Download Statusbar (better than downloads in a separate window)
Flashblock (essential for slow connections)
Stumbleupon (staves off boredom)
Titlesave (save page as the pages title)