For AVC + Vorbis use MKV, for AVC + AAC it doesnt really matter, but if all you mux is that MP4 seems more logical.
It also depends on the tools you want to use after that, and what playback support you would like (the type of the audience, OS, software installation skills, etc).
As i said i will use a htpc or similia. So ffdshow + mpc would be my preferred choice. BHH
They I would go for MKV. More customizable.