You can drop a time coded text file into the Verbatim transcriber. Just format the timecode entries the same way that CatDV does. That way all the code references will carry forward.
Are you talking about doing open captions on the files?
I use Sublime Subtitler to create and lineup (spot) subtitles and open captions and such. I can do everything I need as far as formatting and timing and then export the files in a variety of formats.
Non-linear: all the time and nothing but.