Instances where the Muppet characters interact with animated characters (whether traditional, stop-motion or computer generated) in the same physical space onscreen.

Picture Production / Description
Incredible shrinking weirdo1
Muppet Babies: "The Incredible Shrinking Weirdo"

This episode features a scene where a live-action adult Kermit interacts with an animated Baby Gonzo. A clip from The Muppet Show (episode 223) was used, with Frank Welker dubbing new lines for Kermit and with Baby Gonzo matted into the scene.

Food11
The Jim Henson Hour and Muppet*Vision 3D

Waldo C. Graphic, a computer animated being, interacts with the Muppets in both productions.

Celeb.mickey
The Muppets at Walt Disney World

Kermit the Frog and the gang interact with an animated Mickey Mouse in his office.

Elmopalooza-ToonFrog
Elmopalooza

An animated frog (animated by Sally Cruikshank) appears briefly alongside live-action Kermit, Jimmy Buffett and their frog band during "Caribbean Amphibian."

EWDrawer
Elmo's World

All of the furnishings Elmo interacts with in his room - Door, Shade, Drawer, TV and Computer - are computer generated. In the 2017 rebooted segments, Elmo interacts with a two-dimensionally animated character, Smartie.

HoraceKermit
Kermit's Swamp Years

Kermit's interactions with Horace D' Fly.

Note-Elmo
Sesame Sings Karaoke

Elmo interacts with an animated music note in the framing material.

ThatSong07
What's the Name of That Song?

A lengthy scene of the video sees Elmo and Super Grover interacting with animated numbers and letters.

Samghost
A Sesame Street Christmas Carol

All of the ghosts Oscar the Grouch encounters during the special - Rhubarb the Grouch, Christmas Carole and Sam the Super Automated Ghost of Christmas Future - are computer animated.

Twiddlebugs-Elmo
Twiddlebugs

Interactions with Ernie in the opening of the 2006 animated segments and with Cookie Monster in a promo for sesamestreet.org.

321letsgo1
3, 2, 1 Let's Go

Interactions with Abby Cadabby and Looky Lou.

Velvet
Elmo the Musical

Elmo's co-star of the segments, Velvet, is computer animated. Several of the characters appearing in the segment are computer animated as well, including Moby Pink, the Rhombus of Recipes and Hetti the Yeti.

See also