Don’t think anyone has mentioned this one yet … "All good things … ". It’ll take you a while to get there as it’s the finale of the whole show in S7.
It may not be the best episode or even my favourite, but I adore it as a finale for the show and basically think of it as my favourite finale of any show (anyone care to provide a better one?).
Otherwise I’ll plug “Cause and Effect” (5th season). A great little piece of science fiction in a stand alone episode.