What I have is a bone stock foobar with the APE plugin/DLL file. I also have lame.exe somewhere on my HD (for MP3 conversions). When I want to convert say a directory full of APE files, I just add that directory to the playlist. Then I select them all, right click, and there is a "convert to..." selection. In there is MP3, or WAV, or what-have-you. Choose a destination directory and foobar goes to work.
This is very useful for converting FLAC to MP3. I keep my entire ripped music collection in FLAC on one harddrive, and MP3 on another (for use on the Shuffle and future iPhone). So I rip all my CDs in EAC to FLAC and put them in my "Music 2" directory. About once a month or so I dump the entire "Music 2" directory into the foobar playlist, and convert then all to 256kbps VBR LAME MP3, which I put in a temp directory called "asston of mp3s". Then I add those MP3s to my iTunes library (I have the box checked to automatically copy and organize MP3s added to the library). Then I delete all the MP3s out of the "asston of mp3s" directory, and move all the FLACs from the "Music 2" directory into my "Music 1" directory. Then the process begins again!
Its a tidy system, I'm quite pleased with it.