From Eeebuntuwiki

Keep all your programs after upgrade to 3.0

This time round there is no dist-upgrade path from Eeebuntu 2.0 to 3.0.

For you to keep all your currently installed programs and make it as easy as possible for the new install :

start up Synaptic and go:

File > Save Markings and choose a file name along with a location (like a USB drive) that you can use when you have installed your new system)

This file contains a list of all your currently installed packages, and when you have installed and booted up your new system (and configured your repositories to the best for your location ) then start up Synaptic and go

File > Read Markings and point it at your saved file ensure you tick the "Save Full State" option also, and after that has completed then select Apply to kick off the download & installation of all of those packages you had installed previously!

You will still have to do any special configuration changes that you had on the old system, but at least all of the packages are now in the new system.

Also Backup your sources

Note:- Don’t forget to backup your sources before you reinstall.

sudo cp /etc/apt/sources.list ~/sources.list.backup

Otherwise if you have added any PPAs or other sources, this tip won’t work.

Just save the files onto your USb and back them up. Once youve done the install of EB3 your setup should be easy!