When The Doctor *ahem* 're-modulates his vocal chords' with Fluttershy to activate the Hervoken Charm Cube. Try to imagine David Tennant speaking in Andrea Libman's 'Fluttershy' voice without laughing.
Pinkie Pie's ability to dumbfound the Doctor is both hilariously in-character and believable.
The Doctor's reaction to his ponification
"I've heard about regenerations going wrong before, but never one that ended in...pony!"
Pinkie Pie "advertising" the summoning charm for the S'Muz, which caused all the ponies that heard it to completely crack up:
"Warning: use of summoning charm can cause vertigo, nausea, and may unleash an malevolent cosmic monstrosity upon all reality; do not use under any circumstances," Pinkie Pie said in her best advertising voice.
Rarity's reaction to the TARDIS.
Rarity: It's so... tacky!
The Doctor: What?!
Twilight's computer is programmed to show a virtual Pinkie Pie whenever it comes up with something that doesn't make sense. Think about that.
Virtual Pinkie: Nonsense is what sense sees when it looks in the mirror!