I've been giving this some thought since it was first posted, but it's really tough for me to come up with a real top ten, partly because it's hard to know which versions of the shows I should use. There are episodes I love individually that I think aren't well-served by the 'movie' reconfigurations, as well as 'movies' I love that can just as easily be treated as two episodes each.
Most importantly, of course, each viewer will have his/her own favorites and non-favorites, and I don't know of any polls that have been done to assess the 'consensus' views on which are the truly great episodes.
All that said, I think I'd have to go with Oganga, the Giver and Taker of Life as my favorite installment (to use the form presently available on DVD).