I know The Muppet Movie is the runaway leader here (and I voted for it as well) but I can't tell you how happy I am to see the votes spread around, and I'm overjoyed that The Muppets is second (so far) in this poll. It's third on my personal list (behind TMM and GMC) and I think it's a wonderful film that has earned its place, and then some, in Muppet history and even movie history in general.
Why is TMM still my favourite, then? Where do I begin...incredible music (the best in any Muppet production IMHO), the organic feel of the characters in real-life outdoor settings, the fabulous celebrity cameos, great writing (the fourth wall isn't just broken, it's demolished), a reverence for the movies balanced neatly with the willingness to send them up, and a genuine warmth that launches itself with "Rainbow Connection" and remains solidly rooted throughout the picture.
Also - and I realize I could get flogged for this - I like the idea that most of the movie centres on just a few characters. Between the opening sequence with all the Muppets in the screening room and the arrival of the Electric Mayhem in the desert, we never see more than five Muppets at once, and there are a few stretches with only one Muppet onscreen at a time. I think that gave us a chance to bond with these characters and get to know them a little better, and to allow them to bond with each other. You don't necessarily see that in the other movies, and certainly not in the hectic pace of the TV shows.
There's certainly nothing wrong with Muppet crowd scenes (especially the big Muppet reunion for the "Life's Like a Movie" bit at the end) but I'm glad TMM gave us, among many other things, the chance for some rare insights into Kermit, Fozzie, Gonzo, Rowlf and Miss Piggy.
(Also, I still giggle like an idiot at Big Bird's cameo, over three decades later...)