While our MP3 collection is impressive (and legal), it is useless for work in After Effects because MP3 files use heavy compression to reduce file size . When you throw away 90 percent of the information, then try to render out to a new format, you get problems. MP3 files will result in pops and clicks in the audio track. Don't use them for more than a temp track. If you had hopes of using AAC or WMA files, they won't even load.
The best solution is to stick with AIFF or WAV and encode at the settings you are going to use for final file output. You can convert an AAC or MP3 file to a .mov or .aiff file with QuickTime Pro. QuickTime Pro is actually a great program to have and well worth $30. For more information or to download the cross-platform pro player, go to http://www.apple.com/quicktime.