You should have some experience with (deskop) Linux and webOS to follow this how-to.
If you just want to backup /media/internal and not any apps, follow this instead. I've written this how-to mainly to share my experience on how to mount cryptofs in recovery mode (and how to get the cryptofs key), so that you can backup your apps as well.
First, setup Meta-Doctor on your desktop Linux (or OS X, haven't tried it though) by cloning the meta-doctor git-repository. After that, you need to run the make command as described in step 2 of the wiki article.
Then boot into recovery mode.
Now run this command from the meta-doctor directory (of course adjust DEVICE and CARRIER):
After it's finished, you should see the boot logo. The device won't boot, it's in something like a "special recovery mode".
make DEVICE=preplus CARRIER=wr memload mount
Now connect to your device using novaterm.
In novaterm, run these commands:
Download the attached file "cryptofs.zip" and extract it (alternative url: cryptofs - no extraction needed).
mount -o remount,rw /
mount -o remount,rw /tmp/media/
mount --bind /tmp/media/ /media/internal/
Then run on your computer (from where you downloaded/extracted the file):
Back in novaterm:
novacom put file:///usr/bin/cryptofs < ./cryptofs
(You should see output saying "Enter password:", just ignore it. If you don't see it, it's likely that something went wrong.)
chmod +x /usr/bin/cryptofs
Now, open the meta-doctor Makefile in a plain text editor.
with If you don't want to include the encrypted .palm folder in the backup, also replace
( novacom -w run file://bin/tar -- -C /tmp/media/ --totals -cf - . ) | \
Finally, run this in your meta-doctor directory (again, adjust DEVICE and CARRIER):
( novacom -w run file://bin/tar -- -C /tmp/media/ --exclude=.palm --totals -cf - . ) | \
Now, you should have a directory called "meta-doctor/clones/*subdir*/" with the backup files contained.
make DEVICE=preplus CARRIER=wr backup
Your "USB partition" (/media/internal) and your apps folder is included in "nova-cust-image-castle.media.tar.gz". The decrypted /media/cryptofs folder (where your applications are in) is in the folder ".cryptofs" of the mentioned archive.
An easy way to turn off your device is to unplug the USB cable and pull out the battery (though this only works on phones).
I hope this helps some, if you have any questions, feel free to ask!