I had a similar problem to this, and wrote a recursive script to fix it. It's not 100% fool-proof, but will in essence chmod -x everything except your folders.
You can find a rather poorly documented detail here: http://www.kaear.co.uk/default.asp?pageID=33
(Under "Massively recursive chmod command")
As an aside, the chmod string must in the numerical form, and I would suggest picking something like the following:
644 = rw-r--r--
640 = rw-r-----
600 = rw-------
Give me a bell if you need any help!