Freakazoid and his costars had a few appearances outside of his own series.
Animaniacs
This Pun for Hire (Episode 77; 11/04/95)
Yakko, Wakko & Dot are operating a detective agency. Freakazoid (voiced by Paul Rugg) wanders in, looking for the set for his show. He runs around, making silly faces. Dot tells him that there's been a change: he is the third door on the right, Stage 12.
The Big Wrap Party Tonight (Episode 82; 2/24/96)
Freakazoid has two quick cameos, waiting outside the water tower, and then standing inside at the party. Both times, he is next to Mr. Director (an Animaniacs character also voiced by Paul Rugg).
One Flew Over the Cuckoo Clock (Episode 83; 9/07/96)
Slappy Squirrel's TV Guide has Freakazoid on the cover.
Hooray for North Hollywood (Episode 95; 1/03/98)
A miscolored framed picture of Freakazoid is on the wall in Thaddeus Plotz's waiting room.
Pinky and the Brain
Star Warners (Episode 65; 11/14/98)
In the Pinky and the Brain series finale, the cantina band at Mos Eisner is made up of Freakazoid (drums), Bo-Ron (bass) and Fan Boy (accordion). They play a groovy mashup of the Freakazoid! theme song and John Williams's "Cantina Song" from Star Wars Episode IV: A New Hope. Freakazoid does rimshots when Slappy Squirrel and Yakko Warner make jokes.
Pinky, Elmyra & the Brain
Mr. Doctor (Episode 11; 3/13/99)
Shad Equippo the alien gets picked up on his way to Comic Con by a van with the Freakazoid! logo on the side (accompanied by a sample of the Freakazoid! theme mixed in with the Pinky and the Brain outro).
Other
In the Pinky and the Brain short "Ambulatory Abe" (Episode 12, originally aired 2/25/95), Pinky refers to Washington, D.C. as the "home of Freakazoid!"
In the Pinky and the Brain short "Brain Drained" (Episode 32, originally aired 9/26/97), Brain interviews Hollywood writers to come up with new world domination scenarios. One writer suggests that Pinky & Brain could get sucked into the Internet.
Gasigo (from "Heroboy") plays a key role in the plot of the Pinky, Elmyra & the Brain episode "Better Living...Through Cheese" (from Episode 2, 9/26/98).