Nero is the last major "holdout". I got them to add support for reading .M4A files, but they have been so far dragging their heels on giving their users the option to save (encode) with the .m4a extension. Hopefully, this soon will change.
Winamp 5.03, Apple iTunes and RealPlayer 10 all encode to files with the .m4a file extension by default for MNPEG 4 Audio files. Also it is interesting to note that they also all use .M4A "out of the box" as their default preferred codec/format unless the user changes the setting for audio codec. Compaact gives users the choice of which one by default to use, .m4a or .mp4.
So even though .mp4 is the official mpeg extension, M4A is allowed under MPEG spec rules. Due to its "common use" M4A has now seemingly surpassed .mp4 in popularity for applications encoding MPEG 4 Audio files.
Also, since M4A means MPEG 4 Audio (only), it is bit more descriptive than .mp4 which can mean audio, audio & video or just plain video. It causes much less confusion among media player software and hardware to use M4A in my opinion. I use to launch video playback software every time I tried to play a .mp4 audio files...
