In "D.W. and Dr. Whosit", the Doctor Who-like tv show Dr. Whosit features a cyber-manatee. This isn't technically a manatee appearance, since the creature more closely resembles an orange elephant.
"Wetlands" (Season 3 Episode 17) shows manatees as an example of endangered species in the wetlands.
"Marine Mammals" (Season 4 Episode 3) contains footage of manatees.
The Fuzzytown Friends' teacher, Mr. Kelly, is a recurring manatee character.
"Mermaids and Manatees" (Season 2 Episode 6) features a manatee character named Matilda and her calf Marlon.
Manny the manatee medium (who looks more like a crocodile crossed with a hippo) appears in "The Icky Factor" (Season 4 Episode 2).
"The Cow Show" (Season 3 Episode 2) features manatees in the Everglades.
"Koalas and Wombats: the Untold Story" (Season 4 Episode 5) mentions manatees as a relative of the elephant that is adapted for finding food in the water.
"Sam the Sea Cow" (Season 10 Episode 3) is about manatees.
In Episode 3032, the segment "Under the Sea" contains footage of a manatee.
In Episode 3069, the Creature Feature included the song "I'm a Manatee", sung by Christopher Cerf. This segment is repeated in Episode 3188.
Episode 5221 contains an animated segment called "8 Manatees".
"Swimming" (Season 1 Episode 6) shows West Indian manatees, well, swimming. :)