* "First of May".
** A number of fans were inspired by this song to create-in a strange, fantastical hybrid of this trope and CrazyIsCool-the "First of May Olympics." You can probably guess what that entails.
*** [[AreYouPonderingWhatImPondering But how do you get a red-breasted robin]] [[ComicallyMissingThePoint to sing "Ooh, child"?]]
* "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!"
** "[[AffablyEvil We're not unreasonable,]] I mean, [[EvenEvilHasStandards no one's gonna eat your]] [[EyeScream eyes.]]"
* "And he knows someday, [[Creator/TomCruise he'll]] have to play/[[RefugeInAudacity an old retarded grampa...]]
* "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....
** And then all the Website/YouTube users started commenting on how "no doll tells me how I make my tea".
* The second verse of "Skullcrusher Mountain". Yes, the one about the half-pony, half-monkey monster.
** Don't forget "I see you've met my assistant, Scarface".
* 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 bites from the song over a bass line. Depending on the listener, it's either annoying or hilarious to hear 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 Franchise/SuperMarioBros theme. And even ''more'' recently, he's been using said theme as a transition to his next song... [[spoiler:"Want You Gone", from Portal 2]].
*** At PAX 2009, the song takes a wonderfully meta twist by breaking off into the bridge of Music/TheyMightBeGiants' "Particle Man", which is itself often replaced by covers of other songs when TMBG preforms "Particle Man" live.
* His cover of "Baby Got Back". Mostly because of the genre he chose to cover it with. Think 1960s acoustic folk-rock.
* In "The Future Soon":
-->She would look the same
-->Except for bionic eyes
-->She lost the real ones in the [[HeelRealization robot...wars...]]
-->I'll say "I'm sorry" and she'll say "it's not your fault..."
-->''{{Beat}}''
-->"...or is it?"
* On a similar note, in "Better":
-->And you look like a victim of a surgical crime,
-->A little [[Franchise/StarWars Darth Vader]], a little [[Franchise/{{Transformers}} Optimus Prime]]...
* Which means Judah the Hammer... Judah the Hammer...
* "Chiron Beta Prime", possibly [[OverlyNarrowSuperlative the best folk Christmas song to incorporate a]] RobotWar ever written.
* "Kenesaw Mountain Landis", a song about the [[http://en.wikipedia.org/wiki/Kenesaw_Mountain_Landis First Commissioner of Baseball]], opens with a claim that he was "seventeen feet tall and had a-hundred-and-fifty wives" and only gets more baffling from there. The real kicker is the final verse:
-->[[http://en.wikipedia.org/wiki/Shoeless_Joe_Jackson Shoeless Joe]] left baseball and became a [[Music/JoeJackson famous popstar]]
-->And he asked the musical question [[http://en.wikipedia.org/wiki/Is_She_Really_Going_Out_with_Him%3F "Is She Really Going Out with Him?"]]
-->He had a couple albums and a comeback in the 80's
-->But he never won a Grammy and he never was the same
-->And he never could be satisfied with critical acclaim
-->Cause the critics all confused him with the great Music/ElvisCostello
-->Yes the critics all confused him with the great Elvis Costello
-->
* The skit in the middle of "The Princess Who Saved Herself":
--> '''Princess''': "Hey Adam, tell me if this sounds like a phone hanging up!"\\
(Click)\\
'''Prince''': "Yeah, it totally does! [[LateToThePunchline H-hello]]?"
* From "I Feel Fantastic", the line "All I know is the steak tastes better when I take my Steak-Tastes-Better pill!"
* From "Soft Rocked By Me": "You will be soft rocked by me / I'll use the [[LampshadeHanging passive voice]] to show how gentle I'll be...."
* After ''Series/{{Glee}}'' used his arrangement of "Baby Got Back" without his permission, Coulton re-released his version as a "cover of ''Glee'' cover" as a TakeThat.
* "Dance, Soterios Johnson, Dance": The very notion of an NPR newscaster leading a secret double life dancing wildly all night in clubs is funny, but the fourth verse doubles down by having ''Terry Gross'' turn out to be doing the same.
* "Betty and Me": After the setup, the whole second verse counts. You begin to Betty's point of view on the issue.
-->Betty was pretty firm about our baby being human\\
I said we should give him wings and a nice prehensile tail\\
He could travel with the circus\\
Making money, making friends with clowns\\
Betty said that's stupid\\
And for God's sake would you turn that TV down?
----