The question is in the topic!
using what program? encoding to what format? I could answer ac3 using soft encode, but that might not have anything to do with what you're asking . . .
mp3, aac, ogg, mp2 ..........
MP2: Stereo only! Joint Stereo destroys it completely MP3: Stereo preserves it garanteed, Joint Stereo preserves it most of the time
Any knowledge about ogg and aac?