I don't know about my all-time favorite, but the last two are pretty up there. I love seeing Scott Bakula on T.V. again and I thought him being Chuck's dad and Orion was a pretty solid plot line.
Other than those, the missile command episode was pretty awesome. And the Halloween episode with him and morgan dressed as the sandworm from dune was a good one. It's hard to pick just one. The show really is that good.