The scene where the Bishop proposes a toast to Primus, Septimus and Tertius, unaware that someone has poisoned the wine:
Bishop: (toasting the princes) To the new King of Stormhold. Whichever of you fine young men it might be.
The Princes: To the new King of Stormhold. (They acknowledge him and drink. Seconds later, the bishop's face contorts, and he collapses, dead. They look uncomprehendingly at their cups, and then eye each other suspiciously)
Tertius: Hmmm. (He breaks the atmosphere with a laugh. He suddenly starts wheezing and collapses, dead)
Septimus: (to Primus) You! (Septimus clutches his throat and chokes on the poison, and falls down. Primus' eyes light up in realization that he is now the future king of Stormhold. He picks up the crown reverently. Just as he is about to put it on his head, Septimus suddenly bursts out laughing and stands up sporting a wild grin)
Septimus: You really thought you were king!
Primus: (crestfallen) You killed the bishop.
Septimus: No, Primus, I think you'll find that you killed the bishop by drinking out of the wrong cup. (Beat) Oh look, once you've finished wrestling with your conscience, may I suggest you return to your chamber. Leave the quest for the stone to me.
Tristan is turned into a mouse by Ditchwater Sal. Then there's Yvaine's reaction: she first tries to punch and kick Sal, only to be foiled by a spell Lamia had put on Sal a few days earlier to keep Sal from seeing or touching the star. Upon realizing she's virtually invisible to Sal, during the ride, Yvaine says, "Would I be correct in thinking that you can neither see nor hear me? Then I'd like to tell you that you smell of pee! You look like the wrong end of a dog! And I swear, if I don't get my Tristan back as he was, I'll be your personal poltergeist!"
The not so bloodthirsty pirates. They were a pretty funny bunch.
Yvaine: But of course! Nothing says 'romance' like the gift of a kidnapped, injured woman! I'm not going anywhere with you!
Bernard, transformed into a woman, is seen sneaking looks at Yvaine in the bath. This is topped later, when he tries to serve poisoned wine to Tristan. Tristan asks for "her" name in the stables and "she" replies, in a very deep masculine voice, "Bernard".
The whole pirate fight with Septimus, when he barges in on Captain Shakespeare dancing◊ in drag◊ to "The Cancan Song" (complete with a flat "What the◊ hell is this◊?" reaction), and said music continues through the upstairs fight as the background soundtrack, with swords clashing in time to the music.
Though the actually fighting between Shakespeare pirate crew and Septimus's men is also a moment of awesome for the crew.
And followed by a moment that mixes funny and heartwarming.
Pirate: It's alright, captain. We've always known you was a whoopsie!
Septimus' response to his father's not unreasonable suspicion that he offed his missing sister Una, whom we know is Ditchwater Sal's slave and Tristan's mother: "Why would I kill my sister when these two cretins are still alive?"
Every time the ghosts of the dead princes appear onscreen. For instance, after Secundus dies, his ghost encounters the ghosts of Sextus, Quartus and Quintus. Their bickering is over-the-top hilarious. Or the fact that a lovemaking scene at the Slaughtered Prince is implied by Tertius's ghost telling the others "Come and see this!" and the other ghost calling him a pervert.
The trading scene where Captain Shakespeare is fencing lightning bolts through Ferdy. Shakespeare wants to sell for a very firm price, but Ferdy refuses to budge:
Captain Shakespeare: So! Name your best price.
Ferdy: For 10,000 bolts?
Captain Shakespeare: 10,000 bolts of finest quality Grade A.
Ferdy: Yeah, but it's difficult to ship, isn't it? Difficult to store. If I get the revenue man in here sniffing around. Uhmmm... Best price: 150 Guineas.
Captain Shakespeare:[to his crew] Gentlemen, put the merchandise back on board and prepare to sail.
Ferdy: Whoa, whoa! Hold on. Hold on. One minute, Cuddles. 160? 160.
Captain Shakespeare: Seeing as I'm feeling particularly generous today, I'll settle for 200.
Ferdy: 200? Okay, you're having a laugh. [laughs] Have you had your head in that? Has he been staying up where the air's too thin? [emits a "cuckoo" whistle and lifts his hat off his head to emphasize it]
Captain Shakespeare:[darkly] You're being very rude.
Ferdy: Not any more.
Captain Shakespeare: 200.
Captain Shakespeare: 200.
Ferdy: That's not negotiation! I'm changing my number, 185!
Captain Shakespeare: Did I hear 200?
Ferdy: From you, you did. Yeah.
Captain Shakespeare: You said 200?
Ferdy: If I did, you're a ventriloquist. Okay, 195. Final offer.
Captain Shakespeare: 195 it is. [they shake hands] So, with sales tax, that's... let's see... 200.
Ferdy: [resignedly] Brilliant. Put it in the back.
When Septimus finds Primus's dead body, it's awfully funny to see that while Lamia has used her magic to get rid of the inn after her attempt on Yvaine's life failed, she did not bother to destroy the bathtub.
When one of the witches animates Septimus' corpse to fight Tristain, the other six dead princes turn to look at Septimus. The look on his face is somewhere between "WTF?" and "Well don't look at me."