The "Making of..." programs are chock full of gags, spliced in between the more serious scenes of Talking Heads. Also the end credits. Oh, the end credits. Not really laugh-out-loud funny, more amusing. Like the production crew filming the animals as if they were actors, or the Earth tremors at the end of the Cretaceous turning out not to be the results of the meteor impact, but a random dromaeosaur construction-worker jackhammering the place.
"The activity in its gut produces a lot of excess gas."
A snake starts keeping an eye on the baby T. rex at one point. And then they get too close for comfort. The narrator's response?
"The snake does not like what it can see."
The reaction from the Ornitholestes when he finds out that his former prey, the baby Diplodocus are all grown up. Special mention goes to the way one of them turns to look at him and bellows as if to say "who's the big guy now, punk!?"
All the moments of Camera Abuse, which typically happen Once per Episode, are this, though they add a sort of realism to the presentation as well. Especially when the indricothere calf runs the cameraman over.
You can practically hear the cameraman shouting "nice boy! Nice indricothere! NO! AHH!!!" or something to that effect.
In one of the trailers for the 3D movie, one of the Azhdarchids forgets it can fly and almost falls off a cliff. And the other two just sit there, as if to say "You can FLY you idiot!".
In "Giant of the Skies", we have a moment featuring an unfortunate Tapejara which ended up perched next to a massive geyser. If you look closely, you can even see him shaking water off of his wings when he gets splashed!
In the film, Alex gives a lecture about the Gorgosaurus, but he has to cut it short because he can't stop laughing about its tiny arms.
Patchi and Alex argue about the "dive" the former had done in the river...which was actually him and Scowler falling in during the Gorgosaurus attack. Heck, they even rewind the scene a bit!
When Patchi leads the herd off the icy lake, he starts pushing trees down, saying at one point, "Take that, random tree!"
The Troodon gets a hilarious Oh Crap look when Patchi stops him from stealing the eggs.