I found the iPod Shuffle Database Builder tonight. It looks like a super simple way to deal with MP3 files on my iPod Shuffle. GTKPod had worked okay for me in the past, but shuffle-db looks to be a good bit easier.
I hadn't ripped any CDs since upgrading to Dapper. The steps I took to enable MP3 encoding under Breezy seemed to have been lost in the upgrade, somehow. I read this, this, and this. I tried using the Marillat version of gstreamer0.8-lame, but it didn't work any better than the Dapper-supplied version. Sound Juicer extracted the file, but left it as a 50 meg unidentifiable "data" file on my hard drive.
It wasn't until I read CDRipping on the Ubuntu wiki that I discovered that I was missing a vital package: gstreamer0.10-plugins-ugly-multiverse.
If you upgraded from Breezy to Dapper, you might need to execute
sudo apt-get install gstreamer0.10-plugins-ugly-multiverse. Then follow the instructions for adding the appropriate gstreamer pipeline to Sound Juicer, and everything should "just work".