So, I Used a BSA unpacker to unpack the Oblivion - Meshes.bsa into the "Original" folder. Then ran ApplyPatches.bat
I'm not sure how to fix this error ..
Applying patches...

.\meshes\architecture\anvil\altarcloth01.nif.patch
xdelta3: file open failed: read: C:\Users\****\Desktop\New folder (6)\Original\Users\*****\Desktop\New folder (6)\Patches\meshes\architecture\anvil\meshes\arch
itecture\anvil\altarcloth01.nif: The system cannot find the path specified.

This happens to all of the meshes.^

Patches don't work on vista or windows 7 because Microsoft changed the way some of the commands work and it can't get the path right. You'll actually have to pyffi them yourself instead of running a difference check, which is probably better anyway since pyffi has had some improvements since of the comparison data was made.