For Windows? You can try Subrip 1.50b4
http://zuggy.wz.cz/
(the initial OCR training is hard, but after this it works very well).
Or SubResync 2.23 (part of VobSub package)
http://www.free-codecs.com/download/vobsub.htm
For OS X, I saw D-Subtitler, but I didn't try it
http://www.objectifmac.com/dsubtitler.php
I don't know for Linux
Greetings,
jugaor