A number of fans were inspired by this song to create- in a strange, fantastical hybrid of this trope and Crazy Awesome- the "First of May Olympics." You can probably guess what that entails.
"I'm not a monster Tom...well, technically I am... I guess I am!"
"And we'll put this thing to bed...when I bash your head open!"
"Creepy Doll": Now it’s late and you head downstairs/’Cause you just can’t sleep so you make some tea/And the doll disapprovingly asks if you really need that much honey....
The second verse of "Skullcrusher Mountain". Yes, the one about the half-pony, half-monkey monster.
At his "Best. Concert. Ever." show, Jonathan performed a version of "Mr. Fancy Pants". In place of the normal guitar solo, he began playing disjointed audio bytes from the song over a base line. Depending on the listener, it's either annoying or hilarious to here him say the word "Pants" over and over again...and then he plays them so that they form a coherent statement: "Chances are you're/best in/everybody's/pants!" The entire audience erupted into laughter.
Also, he later improved his skills with the Zendrum to the point where he ended up Rickrolling people... and then when that started to become more well-known he switched it up to "Single Ladies."
And, as of recent shows, has been incorporating the Super Mario Bros. theme. And even more recently, he's been using said theme as a transition to his next song..."Want You Gone", from Portal 2.
His cover of "Baby Got Back". Mostly because of the genre he chose to cover it with.