There are two answers to the problem. It depends on if you have a broadband
connection which is easier.

I save the list of all of my installed applications to a text file using
Synaptic, save Markers in the menu. Then I re-install but keep my home
partition as is (one reason to have a separate home partition), otherwise
you need to save the file to a usb key. After installation, I fire up
Synaptic and choose Read Markers and navigate to the text file. It then
proceeds to download and re-install all of my applications. It takes time
and as I said you need a broadband connection with no limits which i have.

The second way is to back your apps up to DVD using AptonCD which is in
the repositories. This method will only work if you are re-installing the
same version. If you are moving to a newer version then use method one. If
you try to install old version apps onto a newer base, then you are likely
to run into dependency errors and destabilise or even break your system. Not
fun!