My favorite Muppet movies would have to be either Muppets Most Wanted or The Muppet Movie (1979). TMM had a wonderful cast, the humor was sharp and witty, every cameo worked really well, all of the characters fit into it very well and had backstories that were very fitting. And the songs were also great. I can't tell you which song from the movie is my favorite, because I love all of them so much. Paul Williams did a perfect job of writing the songs and capturing the essence of the tone of the film, the characters and the emotions of each scene.
But, as great as the MM songs are, The Muppets Most Wanted songs are complete perfection. You can't get any better than "Something So Right", you can't get any catchier or more Muppety than "We're Doing a Sequel". Music aside, MMW was a really funny movie. I loved all the human cast members in it so much and Constantine is literally the best character to ever appear in a movie. Plus, the writers really made that overused evil doppelganger story work.