It's a tricky question, some definitions will include Creature Shop stuff, but I think many of their things don't really count. Although some Creature Shop stuff, such as Ghost Of Faffner Hall should. Not least because Ghost Of Faffner Hall, The Animal Show, and, Mopatop's shop all not only used some Muppet-style puppets, but even reused some of the minor puppets from TMS itself. (In some cases even with the original TMS puppeteers - for example Frank Oz doing Sam The Eagle on The Animal Show, while I'm sure Louise Gold must've done her Fish-Singer on Faffner Hall, and could she have reprised her infamous monster imitations on Faffner Hall? who knows....)
Generally, I'm not sure about counting such purely Creature Shop ventures as Teenage Mutant Ninja Turtles, Labyrinth or Dark Crystal. But there are situations where one might include them for brevities sake. For example on my fansite about Ms Gold, I've used the catagory 'Muppet Work' to define all her Henson puppeteering, as opposed to her performances for Spitting Image, Roland Rat and other distinctly non-Henson projects.