Another approach is not to patch nixpkgs at all, but just to "override" packages in Nixpkgs outside of the repository, and build them from your own project directories.

A simple example: I wanted to build FFMPEG, but with non-free libraries enabled (which is not the default). Rather than edit "ffmpeg-full" in the nixpkgs repo, I just overrode it:

    # default.nix (in some project directory; call "nix build -f ." to run it)
    with nixpkgs;
    {
      my-ffmpeg =
        let overrides = {
        nonfreeLicensing = true;
        fdkaacExtlib = true;
        ffplayProgram = false;
        qtFaststartProgram = false;
      };
      attrs = {
        name="my-ffmpeg-" + ffmpeg.version;
      };
    in
      ffmpeg-full.override overrides // attrs;
    }