I don't really have a "Top 5" list, but here's a list of my favorite Henson shows:
*Sesame Street
*The Muppet Show
*Dinosaurs
*Muppets Tonight
..and I've only seen a couple of episodes of Fraggle Rock right before the Odyssey Channel got replaced by the Hallmark Channel and I also heard FR songs on Muppet Central Radio. It's been a long time since I've seen Muppet Babies.
Other Henson shows I've seen:
*The Wubbolous World of Dr.Seuss
*Farscape
*Mopatop's Shop
*Construction Site
*The Hoobs
*Telling Stories with Tomie dePaola
*Animal Jam
*Jim Henson Presents:The World of International Puppetry(the episode with Richard Bradshaw)
*The Fearing Mind(saw only one episode)
..and I have seen clips of Family Rules,the animated version of Fraggle Rock,Jim Henson's Greek Myths,Mother Goose Stories,CityKids,The Secret Life of Toys,Dog City,The Storyteller,and The Ghost of Faffner Hall at the old Henson.com site
I've seen Sam and Friends clips on several specials(including the A&E Biography special on SS)and at Henson.com
I saw a commercial for Brats of the Lost Nebula on the Hallmark Channel(in Asia)-they were advertising stuff that was on the Kermit Channel and BOTLN was on the
Channel.
I have seen a clip from The Jim Henson Hour-the one where Fozzie is a weather reporter on "Good Morning America" on the "Time and Again" special on Jim Henson a few years ago. Also read transcripts from the show at Tough Pigs and saw the first 20(or so)seconds of the opening number.
As for favorite Henson special--it would have to be A Muppet Family Christmas,the first Henson special I've seen.