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Both ScreenFlow (Mac-only) and Camtasia (Mac/Win) support subtitling. Both are excellent screencast applications but I prefer ScreenFlow because it creates MPEG-4 files whereas Camtasia requires Flash for subtitles and that pretty much rules out mobile.
If these screencastsare made with some other, less expensive apps, I suggest using free, open source apps. There are many but I prefer Jubler for creating subtitles and Subler for installing them in MPEG-4 files. These are Mac apps.
I've recently come across CapScribe which is free to education and plan to look it over carefully. It looks very promising: http://www.inclusivemedia.ca/services/capscribe.shtml This is also Mac-only.