February 28, 2005 - A Palisades Toys actions figure of Gonzo was used in a shot of Michael Jackson's jury, along with Corey Feldman and Jabba the Hutt. After the shot Jon commented with, "That was Gonzo! Gonzo couldn't get out of jury duty!"
April 14, 2005 - Reporting on the 36th season premire of Sesame Street, Jon mentions the episode's dedication to healthy eating and names a few guest stars, and reports on the new "cookies are a sometimes food". "It's perhaps the biggest behavior change in a show regular since 1974, when the then popular Smokey Monster then switched to filter tips. Smokey tragicly succumbed to cancer of the googly eyes in '83. We miss you, Smokey."
Starting in 2005, the show began concluding with a "check-in" to the show's spin-off The Colbert Report which airs directly following the program. On the June 19, 2006 episode, Stephen Colbert's show description paid homage to The Muppet Show, even including a video clip of Sam the Eagle.
- Stewart: Welcome back to the program. Before we go we're going to check in with our good friend Stephen Colbert at the Colbert Report. Steven.
- Colbert: Thanks Jon. Up next on a very special episode: space travel, sure it's possible, but for pigs? An update on Scandinavian cuisine with our in-house chef, and then our very special guest star Harry Belafonte will lead Fozzie and the gang in a chaotic, and hilarious, version of the "Banana Boat Song"...Day-O! It's so good even Statler and Waldorf will allow themselves to smile. All that plus a final off-key trumpet note from Gonzo. Jon.
- Stewart: Stephen, it sounds like you have a dubious collection of guests there.
- Sam Eagle: (clip from The Muppet Show) With a few exceptions, the characters on this program are weird and peculiar and not to be trusted.
- Stewart: That's our show, join us tomorrow at 11. Here it is, your moment of Zen.
July 12, 2006 - Jon Stewart features a spot on Pennsylvania Senator Rick Santorum in which his re-election campaign involved distributing flyers titled "50 Things You May Not Know About Rick Santorum." In what Stewart called a fun quiz for his audience, a list of things supposedly found in the flyer were displayed on-screen, some of which are meant to be real, others of which are not. The last in several of these "facts" cites that "Rick is voiced by character actor Frank Oz."
October 30, 2006 - Samantha Bee presented a segment where she re-visted her "home town" in Ohio (despite not actually being from Ohio). She visits a school that she claimed was her "old school". She begins to "reminisce" about her old school days when an administrator from the school asks her who her teacher was. She looked around the classroom and, upon seeing the Think Different Poster with Jim Henson hanging on the classroom wall, hesitantly replied "Jim Henson".
- Muppets: 1, Host: 0 - ToughPigs.com transcript
- YouTube video of Kermit the Frog on The Daily Show