Most likely going to depend on what type of audio was in the original source file. If it was an ac3 track then visualhub would produce a .mov file. It is only able to create appletv files with ac3 tracks in the .mov container. However if the original file contained a dts or a different audio source then it creates a single downmixed audio track, which it is capable of muxing into a .mp4 container. The downside to using visualhub to create a file with an ac3 audio track is that it uses the .mov container which can't be fully tagged with meta-data. For instance you can't add mpaa ratings to a .mov file created in visualhub, as well as some other tags I believe.
For future compatibility, and current development familiarize yourself with handbrake (especially the current development builds), maybe harder to figure out at first but is capable of producing excellent looking/sounding files all in a correct .m4v container. It's also being actively developed so improvements are being made on a regular basis.
