I just made the switch from Ubuntu to Mint, and I recommend you do the following:
1) Make a backup (rsync to an external drive) your entire home folder.
2) When installing Mint use ext4 (it is much faster than ext3)
3) Reinstall any custom applications
4) Restore your files (no hidden or system files)
Let me explain about hidden and system files in your home folder:
1) The switch from Ubuntu 8.10 to Jaunty met with some changes to several applications, including Gnome (you will really like those changes!) causing some incompatibility between hidden files in your home folder.
2) Since you are switching OSes, you might as well take the time to start fresh. Keep the hidden files for occasional reference, but it really is not that time consuming to set up your applications fresh. (I did it after using Ubuntu for 4 years.)
If you have any other questions about migrating, I would be happy to help. By the way, I am very pleased with the switch.