It should, in principle, be possible to just 'tar' everything to a file on the SD card and re-install from there. The good is that it also takes care of not only the applications, but also the /var/lib/dpkg/ structure, which keeps track of what's installed as seen from the apt-get/dpkg programs etc. The bad is that unpacking such a file would almost certainly try to overwrite files that are currently open, and create havoc that way.

My old Sharp Zaurus backup system is simply the above: It makes tar files of it all, and the ROM monitor (or possibly the early-start boot loader, I'm not certain) can unpack the tar file (this avoids the overwrite/live system problem). Works beautifully, after flashing a new kernel I can always reinstall all the rest in one single step, nothing lost. And, as the internal storage on the Zaurus is volatile RAM, I also have to reinstall whenever it runs out of battery.. unlike the N800, so its backup feature comes in even more handy. It should in principle be possible to have an equally good and easy backup procedure on the N800, but it's not there now.