After watching Family guy last night, I found a couple...
In the Pawtucket Pat brewery tour episode, one character was accomplished ninja, Jerry Nelson. Now, I'm not sure they named the character after the puppeteer, or it was a coincidence, or they just couldn't come up with a better name (since he was only one for a collective 20 seconds), but I'm taking it as a refference.
There was another, this one Convincing John posted a while ago, But I'm gonna archive it here...
In this episode about Peter going for sensitivity training after sexual harassment problems at his job, the final scene has The sensitivity training feminist teacher fighting with the housewife, Lois Griffin. They are at this gala party, and a Baker, singing comes out with "Te-e-en banana creme piiiiies!" and promptly gets knocked over.
There was an old man at one point in one episode that looked an awful lot like Statler, so I thought it was a refference, but I guess they draw all their old men to lokk like that...