Well this should be easy since Firefly only ran for half a season. People have often said such and such episode is in their top three, but for the record, what would you pick and why?
For me:
1.) Out of Gas: this episode showed how everyone got on the ship, and how important Serenity was to Mal, and how important Mal was to his crew.
2.) The message: I thought this episode was very powerful, emotionally. The last scene with the funeral and the music gets me every time.
3.) Objects in Space: Jubal Early is an awesome villain, and seeing how Mal completely accepts River as a part of his crew (in fact, almost like his own daughter) was a very powerful and bittersweet way to end the series.