Prepping for clean install

[DarkGob]

I've been away from Ubuntu for a while, and now that I'm returning I'm finally going to go ahead with the upgrading from 9.04. My understanding was that upgrading from 9.04 to 9.10 and beyond would be easiest with a clean install, I just want to make sure I get everything saved and backed up.

Obviously the home folder is a must. I'm unsure about what's the easiest way to save/backup my list of downloaded packages (understanding that I probably won't be keeping all of them as some will be out of date), and I'm trying to remember what else I may have hand-changed outside of the home folder that I might be forgetting (already checked GRUB and sources.list, those seem to be fine). Or should everything outside of /home be considered disposable?

[bondo101]

Use clonezilla and back it up to another usb external drive. clean the drive then use the backup and use the files that you want.

[darkod]

One way to save a package list for clean install that I have bookmarked, is this:
http://ubuntuforums.org/showpost.php?p=7157175&postcount=5

You can also check out a add-on for firefox called Umarks. Google says it is used precisely for creating a package list and that you are even able to select which packages you want installed in the new install, you don't have to reinstall all of them. But I haven't used it, you'll have to dig out more details.

[DarkGob]

How about programs not installed via the package manager? Is there any easy way to get these or must I reply on memory?