I use Quicktime Player Pro to export avi files in an iPhone compatible format. I just need to a) put the subtitles file and the movie file in the same folder (except the extension, they need to have the same name), b) open the movie file, and c) export the movie. The resulting file has the subtitles hardly encoded in.

I'm just waiting for the Quicktime module for Automator that allows to choose which exporting format you need in order to make the things easier.

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