There are so many fine episodes, but I think my favorites -- the ones that come to mind immediately are "New Ground," "The First Ones," and "Fire and Water."
I also really appreciated MS's range of acting in "Need," "Legacy," "The Light," and "Absolute Power" --- not exactly his old Daniel self in those.
I can't think of any episodes of his that I didn't like, and I enjoy watching him in other programs such as Outer Limits and some of the films he's done. The man has a lot of talent and I hope he gets all the opportunites he seeks.