I am hoping that this question would help other ubuntu users when migrating to a newer version of ubuntu. This should have all the info that they need. So please when you answer try to phrase them into points for easy understanding. I understand that some questions that I ask might have been asked before by other users. In that case just provide the links to those questions.

I am running ubuntu 10.10 Maverick Meerkat in case that is important. I can say for sure that a clean install is definitely better than an upgrade since it gives you an opportunity to clean your system and get a fresh start. However some of us like to retain certain software configuration or files etc.

The questions are as follows,

1. How do you save the configuration files of certain application like for instance Thunderbird, firefox, etc...so that you can basically paste in the new version of ubuntu? (Thunderbird for instance has all my mail, so I definitely would like to backup its configuration and then use it the new installation that I do)

2. I have some applications like MATLAB and Maple (Based on JAVA) installed. When I migrate, can I just copy the entire installation folder to the new version of ubuntu? Would it still work as now if I do that?

3. When doing a backup which folders should be backed up? Obviously your personal files would be backup. But other than that, is it necessary to back up stuff in the home folder, /usr/bin etc?

4. I have BURG installed. I am guessing that would be erased when I do a clean install along with the program's configuration and everything. How can I do a backup of it?

5. I am dual booting my ubuntu alongside with Windows 7. When I perform the clean install of ubuntu, would GRUB (bootloader) be removed and in anyway jeopardize my windows installation?

6. Over time I have added a lot of PPA which are of course compatible with my current ubuntu version. How do I make a backup of all my PPA and would they be compatible to the newer version of ubuntu when I restore them?

I hope this covers all the questions or doubts that a user might face when thinking about performing a clean install of his system. If I missed anything please mention it as a comment and I will add it to my answer.