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We wrote about MovCaptioner before, but there have been significant improvements in both the interface and in the type of captions MovCaptioner can create. The website now lists all these types:

Embedded QuickTime Caption Tracks
SMIL Caption Tracks
Flash Caption Tracks
SubRip SRT and SubViewer SUB Caption Tracks
Spruce STL (imports into DVD Studio Pro)
Adobe Encore Caption Tracks
SAMI Caption Tracks [...]

CapScribe is an open-source Mac OS X application to help you add captions and/or audio description to audio and video files.

Some utilities for dealing with subtitles or captions:
SubCleaner
Blurb:
SubCleaner can:

remove unnecessary characters & formatting errors
limit the number of chars per line & the number of lines per subtitle
convert MicroDVD, SubViewer, SubViewer 2.0, and TMPlayer subtitle formats to SubRip (.srt) format.

SubSync
Blurb:
You have encoded your favorite series, a friend sends you the subtitles, but the filenames don’t match, [...]

MovCaptioner keeps repeating a segment of the movie until you are done typing what you hear. Just hit the Return key and it will save your caption and automatically advance to the next few seconds of the movie, allowing you to zip through your captioning tasks in no time flat. You don’t need to be [...]

Submerge merges your subtitle files with your movies, to allow them to be played and watched with players which are not subtitle-aware.