I use ffmpeg (mencoder in the past as well), wrapping it into a shell script, when I need to mass convert audio or video files. I don't see how a graphical user interface would ease the job, but I guess it depends a little on what and how you're doing exactly. A typical script would use find
to create a list of the files to be converted, a loop of some kind in the script to go through them all, and possibly some fine-tuning, for example to get nicer filenames (i.e. .mp3 instead of .xxx.mp3). Though I only convert if it's really "a must", because it won't make the audio quality any better, usually only worse.
Unless you have some really exotic formats, one engine should do for you. For example GStreamer and the plugins, which you are usually able to install with one command. If you feel you keep needing several programs and engines, you're probably doing things with too much complexity
Distros usually do come with some audio system installed out of the box, be it GStreamer, Xine or something else, so all you need to do is install the "non-open/nonfree" plugins for that system, nothing else...
Lastly, as good as it sounds, I wouldn't go about re-encoding all my audio into some open format (especially if I didn't have all the original audio media available for ripping again when needed), because even today very rare cadgets play those formats. It might be a huge work, and if you later end up having to move to another format, it's again a huge work (and possibly means losing quality further). It's a pain in the digital media, but it seems mp3 would be a good bet (and about the only one) if you want to go through the conversion, as most devices will play it (old and new) whereas other formats are less well supported.