AFAIK KDiff3 can not create the diff file, but you can use commandline diff utility or cvs.
If you have for example moodle/ and moodle.original/ directories, go into their parent and issue
diff -ruN moodle moodle.original > myfirst.patch
where r is recursive, u is unified style, N is to include also content of new and deleted files
If you are using cvs, go to you moodle root and type:
cvs diff -uN . > ../another.patch
where the dot is current directory, which means check all moodle files, you can type wanted files or directories too
Applying of patches might be harder, it can be done with patch command, go to your moodle directory and type:
patch -u < path/to/other.patch
and you will be asked into which file exactly to apply the patch, though I do not know exactly how to handle new and deleted files with it
Another way is to use Kompare, it should be able to apply patches.
And yet another is to install PHP Eclipse and use built-in diffing and patching