Sadly, except in a few parts of Europe and elsewhere TMS and Fraggle Rock(arguabley two of the greatest shows in the last decade and a half) are rarely seen anymore. Its a shame.
As for Muppets Tonight, due to the fact it wasnt near as edgy as JHH was 7 years prior, I think perhaps MT remidned folks too much of Sesame Street with its colorful foam characters and lighter variety show format. It did have some great moments...
Pepe and Beaker free style rappin' to impress Coolio(Beaker as the Muppet beat box of course) was just way too funny. Also that Seinfeld Babies was a hoot.
Hopefully that new Fox Muppet Show will be coming before 2004, which should hopefully put the Muppets back in the spotlight.