As of git 1.8.2, this:
MyPrject/WebApp/Scripts/special/**/*.js
Should work according to this answer. It also works for me in Windows 7 using Sourcetree 1.6.12.0 and the version of git that it installs (1.8.4-preview20130916).
To gitignore every file and folder under a directory recursively:
MyPrject/WebApp/Scripts/special/**