You could provide links in a transcript which when clicked take you to the part of the video in question, if you'd like to see it. You could also go the other way, and use a transcript to provide subtitles.
Any ideas on how to make this happen? My intial thought is to exploit pauses and breaks in the sound and map them to sentences, etc. Voice mapping would help too, so you could map a sentence to Paul Graham and another sentence to the interviewer.
What would be pretty cool (actually, REALLY cool now that I think about it) would be desiging a transcript markup language that could be married to a video. Has anyone done this? Why not?
Perhaps Amazons mechanical turk could come in handy here? Would a clone of the mechanical turk specialised on movie transcripts be feasible? Or is it too special interest? (Perhaps most people either understand the words or they would prefer a translation?).
As for syncing subtitles: I don't know the details anymore, but I remember from ripping DVDs that the subtitles come simply in a text file along with the movie. So presumably something like you propose already exists.
Unfortunately they only provide closed service for registered users: http://www.nicovideo.jp/ (Actually they originally used YouTube as a video source and had no access restriction. But they got so much popular that YouTube had to shut down access from their site.)
I'll just need to refresh my japanise ;)
If you want to convince me that your product can do what it says - take the video talked about in this thread, run it through your software and give us a link so we can see what you mean.
I shall be releasing about 12 demos of juwo on my website shortly - hopefully this week. (I work on it in my free time so have been extremely slow this year).