But yesterday when I played around with QuickTime, I noticed that all I need to do is open the movie in QuickTime, and if the .srt/.sub file is located in the same folder as the movie, it opens as well (this is well known). However, after that, all you need to do is save (via File » Save As), and the subtitle track is merged directly into the movie file. No extra software is required.
[robg adds: I haven't tested this one, but I think QuickTime Pro would be required to save the movie.]

