Skullmageddon's Bad Boss tendencies, especially when you break his TV's.
"This is coming out of Williams' salary! ALL OF THEM!
"THAT'S A PLASMA SCREEN! That's expensive!"
"Williams, I'm docking your pay for this!"
"WILL YOU STOP destroying my things?!"
While in Skullmageddon's rocket-dojo, Billy and Jimmy end up outside. How do they survive? By holding their breath of course! But not before making a one-liner about there being no air then sucking in air, WHILE THEY'RE IN SPACE.
The title of the Mission 6 boss: The Expensive Experiment Giant Tank. Then you blow it up.
Mission 7's intro
"What is this? Some kind of lab?"
Mission 7: Some Kind of Lab
In the countryside, when you destroy then monuments, when Billy shouts "Sacrilegious!" in the same excited way he'd shout "Awesome!"
"IDIOTS! DON'T LET THEM NEAR THE GLOWING, RED WEAK POINT!!! (beat) Why does it even HAVE a weak point??? Couldn't you have put a cover on it??!?"
After defeating the Tank, rather than the standard "Billy and Jimmy move forward to Skullmageddon's castle", the tank knocks down the Kill-o-copter, causing it to crash into the tank. This causes a huge explosion that knocks Billy and Jimmy out. Skullmageddon, clearly a little confused, quickly tells his mooks to capture the brothers Lee.
The fourth wall-breaking ending credits song ("Dared to Dream") to Double Dragon Neon, wherein Skullmageddon sings about being defeated by the Lee brothers. The funniest part comes at the 1-minute mark, when he sings "Here's a medal for your victory" and the Achievement Unlocked/Trophy Unlocked dialogue pops up.
He's got plenty of other moments as well:
Right after you press start for the first time in the 360 version, you get an achievement called Skullmageddon's Curse that's worth 1 GS, with the description "Nyah ha ha! Now finish what you have started!": a lot of people like to keep their GS divisible by 5 and the score can only be evened out by getting the achievement described above, which involves defeating him.
Right before you encounter him for the first time, you can find a hair pick from a barrel: if you throw it at him, it'll pin down his hat on his head, making it so that he can't use any attacks that involve removing it until he takes it off while complaining how he could be done in by such a mundane item.
When trying to kill the Lee brothers with a helicopter, he's heard saying "Of course helicopters can fly upside-down; don't be ridiculous. SHRED THEM!" and then proceeds to do just that.
If you pause the game while fighting him, he comments on it in a variety of ways: