We recently had a mobile project with lots of video content, all of which needed to be subtitled and work on the iPhone and iPad.
Many hours of research, hair pulling and frustration later it became clear that the Closed Captioning world is a broken, horrible place to be. We had the videos, we had the transcript but there seemed no way of putting them together in a timely and cost effective fashion. The business model in the closed captioning world (like many others) is make it really complicated so that you either have to pay someone to do it (at a cost of around £10 per minute of video) or buy software with a price tag on multiple thousands that although sounds like the saviour, is actually just makes things even more complex.
The problem? Multiple incompatible formats of subtitles, multiple broadcast formats, all requiring their own solution and no-one place to find out reliable, up-to-date information from. Eventually we got it figured out, a nice in-expense (but not free) way to get your own closed caption service up and running.