After searching around on the net trying to find an easy way to create and apply patch files, I came up with the following free solution that creates linux compliant patches.
1. Download and install patch and diff from the GNUWin32 Project http://gnuwin32.sourceforge.net/packages/patch.htm and http://gnuwin32.sourceforge.net/packages/diffutils.htm

2. Navigate to the place that the exe's were installed (eg. C:\Program Files\GnuWin32\bin)
3. Create a new file called patch.bat and put the following code in the file:

@echo off
"C:\Program Files\GnuWin32\bin\patch.exe" < %1
pause