Is there a program that will let me compare MP3 files since WinABX, ABX, and ABC/HR only seem to work with .wav files? For instance, I downloaded 2 different versions of the same song in .mp3 format and would like to compare the "digitally remastered" one with the "original" one.

Foobar2000 has an integrated ABX comparator. Encoded files are decoded temporarily to a temp folder.

Thanks tigre! Using a comparator doesn't do anything (i.e. modify) to the .mp3 files themselves, right? For instance, when ReplayGain is used, is that applied only to the .wav files that were created in my temporary folder?

AFAIK you can decide if foobar2000 stores replaygain info in the files (default IIRC) or in the database (Preferences -> Database -> [x] Database enabled, [x] Don't write modified tags to files). To be completely sure you can find out yourself by copying some files to a temp folder, replaygain them and using some md5 tool like EasyMD5Creator to check if they're changed.