I dunno about Spy Kids 3-D, but Shrek 3-D was just plain painful to watch. Granted, it made the ride look spectacular and it's an awesome film, but it's definitely not made for the red and blue 3-D glasses you get in cereal boxes.
Muppetvision 3-D I think would be hugely entertaining even on DVD in non-3-D form. Wait, here's an idea. Disney could release Muppetvision and The Muppets go to Walt Disney World on a single DVD set. That would be brilliant beyond brilliant.