We know that these encoders don’t particularly like certain things (things like really fast, sequential transients or songs that are slammmmming 0 dBFS the whole time). So it may be possible to try to prevent some of “yuck” that an encoder induces (especially in mastering)

What I do (and would suggest) is that before you bounce out your final AIFF or WAV for mastering, do a quick bounce of an mp3 and listen to that. (Of course, comparing it to an uncompressed bounce). Since you know that your audience will likely be listening in the mp3/AAC format rather than the uncompressed format, it is definitely a good idea to make sure that your song is well represented in the format.

Additionally – if online retailers let you send in your own mp3/AAC files, do it! In a lot of cases, you won’t know what encoders/settings they are using if they rip your CD. If you can send them higher quality compressed audio, and you can verify that it sounds good, then that is definitely a preferable situation.