I use periscope, which works really good in Linux, but if you are using windows, like me, you can follow the instructions here:
http://code.google.com/p/periscope/wiki ... derWindowsWhen you have it setup, you can create a DOS batch file to have it run when you'd like. You can give the periscope script a top level directory, and it will go through all the sub-directories and find subtitles for all the files you have. It is working really well for me.