Here are what I believe are the Jim Henson Hour episodes that aired in 1989. Twelve are listed here. Originally the special "Sesame Street 20 and Still Counting" was slated to be a part of the Jim Henson Hour, but instead was shown the week before the program premiered. This might explain for the "missing" 13th episode or there could be another one that we don't know about at all.
The 1987 Inner Tub pilot never aired on tv and is 22 minutes long. Since it never aired on tv and isn't a full episode it doesn't count as an episode in my opinion. Episodes with a * didn't air in the US (at least with the Jim Henson Hour bumpers as in the case of Living with Dinosaurs and Monster Maker which were shown on Nick in 1993-1994 and Odyssey 1999-2000).
1. Muppet Television: Louie Anderson, The Storyteller: The Heartless Giant
2. Muppet Television: Ted Danson, Lighthouse Island
3. Muppet Television: The Today Show, The Storyteller: The Soldier and Death
4. Dog City
5. Muppet Television: Bobby McFerrin, Miss Piggy’s Hollywood
6. *Monster Maker
7. Muppet Television: Smokey Robinson, Song of the Cloud Forest
8. Muppet Television: Buster Poindexter, The Storyteller: The True Bride
9. Muppet Television: k. d. lang, The Storyteller: Sapsorrow
10. *Living with Dinosaurs
11. *Muppet Television: Food, The Storyteller: The Three Ravens
12. Secrets of the Muppets