Slightly off topic, but since you brought it up - This is going to be different for each user depending on their needs. With huge storage space options one can keep very large libraries in lossless formats like FLAC or ALAC. The mp3 format still has some benefits when the target is a portable player or perhaps for a car radio. But once the mp3 conversion is made the damage is done.
The best advice that can be made here is to choose one platform to do all of your editing. Mixing software like mp3tag, TRAKTOR, iTunes, WMP, and others to do your tag editing is bound to have issues like this.