Link's line in 'The Rhyming Song' had me laughing for quite a while. Also 'Put Another Log on the Fire' in episode 115, the UK spot with Beethoven's 'Pathétique' in episode 313 and 'Mack the Knife' UK spot too from episode 315. There really is too many to list...
Movie wise... the roll call from 'Muppets Treasure Island', and when they all go up the side of the Mallory Gallery really fast in 'The Great Muppet Caper'. I'll probably think of more after I post this...
Beaker singing "Feelings" to a hostile crowd STILL leaves me rolling on the floor in laughter.
Beaker, The Swedish Chef & Animal doing "Danny Boy" is another brilliant piece of hilarity.
The Cowboy sketch from the Juliet Prowse episode has a lot of funny stuff going on.
The hapless Lenny the Lizard performing "Inchworm" (or is it "Glow-worm?") from the Rich Little episode, ultimately being devoured by a monster (this was based on the old bit Kermit used to do on various TV shows).
"Good grief, the comedian's a bear!" a classic Kermit & Fozzie routine from the Harvey Korman ep. I love how Kermit loses his patience.
Fozzie's "impressions" that all sound the same during one of his stand-up routines.
Fozzie's claim that he could turn anything into a joke ("amoeba!") during another stand-up routine.
Statler & Waldorf's various comments throughout the series.
During the muppets bohemian rhapsody commentary
Kermit is in a phone box
Zoot wakes up
Zoot:"Wha.....oh it's that bohemian thing"
Kermit:"How come I didn't hear you come in?"
Zoot:"Come in?!I've been sleeping here for 3 months!"
Trust me it's much more funnier when you hear it