I would choose neither and remux them to an MPEG-4 Part 14 (ISO/IEC 14496-14) container (known as "MP4").
The QuickTime File Format (QTFF) was the basis for MP4. They offer (more or less) the same support for video, audio and subtitle codecs. However, you will find many devices being unable to read MOV files at all. Playing MOV files natively in earlier versions of Windows is not possible, for example.
Matroska, while being open source, is not standardized by the ISO. This might not really matter—and in fact, it is an open standard—but device playback support for MKV files is only picking up very slowly. It is a promising container format but you will probably never see it being used for any real application, other than sharing video on the web.
The past has shown that when companies build applications or services that are deployed for consumer electronics or any kind of public interest, they rely on well-established standards, which in turn are mostly those published by the ITU or ISO.
Think about DVB broadcasting, which uses MPEG-2, the DVD, which uses MPEG-2 as well, or Blu-ray discs, which use MPEG-4 Part 10 (AVC) video. All video cameras record some variant of MPEG-4 video these days and use storage formats defined in MPEG-4 or strongly related to those (e.g. AVCHD).
Recent initiatives have brought up the discussion about software patents in various video and audio codecs—especially with regard to HTML5 Video—but this is not really an issue with storage formats such as MP4.