diff -r
   --exclude="*~"
   --exclude=".svn"
   --exclude=".git"
   --exclude="*.zip*"
   --exclude="*.gz"
   --exclude="*.tar"
   ...etc

$ find ONE TWO -type f -print
ONE/a/1.txt
ONE/a/2.txt
ONE/a/b/2.txt
TWO/a/1.txt
TWO/a/2.txt
TWO/a/b/2.txt

$ find ONE -type f ( ! -regex 'ONE/a/2.txt' )
    -exec bash -c 'diff -q "${1}" "${2/ONE/TWO}"' - {} {} ;

diff -q ONE/a/1.txt TWO/a/1.txt
diff -q ONE/a/b/2.txt TWO/a/b/2.txt

$ find ONE ( -regex 'ONE/a/2.txt' -o -name b  -prune )
    -o -type f -exec bash -c 'echo diff -q "${1}" "${2/ONE/TWO}"' - {} {}

diff -r <src-dir> <dest-dir> | grep -v directory/sub-directory

$ diff -rq foo.orig foo | grep -vP 'ignore1/|exclude2/' | awk '{print $2}' | cut -d'/' -f2- | xargs -I{} diff -u foo.orig/{} foo/{}