Okay, so I haven't actually done this on my n800, but I have just done it when upgrading a laptop (running ubuntu 6.10)

a) first, before upgrading, run in an XTerm:
dpkg --get-selections > /media/mmc1/packages.txt

This stores a list of packages and their installed status

b) upgrade and restore a backup that contains sources.list

c) In XTerm (running as root) run:
cat /media/mmc1/packages.txt > dpkg --set-selections
apt-get dselect-upgrade


This seems to work pretty well, at least of ubuntu, so maybe it will help here. Of course, for applications that have been installed but not from a repositary (gizmo, for example), it will not help...but in other cases, it maybe okay