Generally speaking a full backup is hardly necessary -- or meaningful -- but here's what I'd do to create and restore "nearly full backup". I haven't done this as-is, but the general idea should be clear.

Backup:
- normal backup with Backup/Restore
- full backup of $HOME: (cd /home/user; tar -cpf /path/to/mmc/home.tar .)
- full list of installed packages: dpkg --get-selections >/path/to/mmc/packages

Note that these steps do /not/ cover dpkg status, diversions or anything like that. Backing up that data can be useful, but generally it does more bad that good. Maemo-specific metadata, such as menu locations of applications etc, may also be missing.

Restore:
- normal restore with Backup/Restore
- restore $HOME: tar -C /home/user -xpf /path/to/mmc/home.tar
- reboot -- some services may be monitoring changes in files, so just in case, reboot
- restore package state (as root): dpkg --set-selections </path/to/mmc/packages && apt-get update && apt-get upgrade

Obviously I take no responsibility for running apt-get manually. I'm not aware of ill effects or running apt-get upgrade, but I'd assume Application manager takes care of certain unspoken rules of Maemo of which apt-get is simply unaware.

If you really need to backup installed applications as is, you can use dpkg-repack to recreate already installed packages. These packages can then be installed with "dpkg -i".