Things failing to hit the godmodder in extremely ludicrous ways.
The godmodder blocking attacks in even more ludicrous ways.note Aegis threw the sun at the altar of power. The godmodder shrunk it until it was the size of a basketball and about as warm as a small campfire.
You should never EVER under any circumstances allow Enter and Return into an operating room, because their first move will always be to try and replace the equipment with sharks, trees, and/or umbrella. On Adventurers' Island they even got separated from the team just so they could stop by a river to catch a shark, never mind the fact that sharks only live in salt water.
While not a Running Gag within Dino Attack RPG, a brief moment in which Elizabeth got rid of a pursuing policeman by telling him there were free donuts in the tavern was a reference to a bizarre running joke in the second Pirates RPG, where Elizabeth would escape from Imperial soldiers by shouting "drinks on the house", a statement which the soldiers would promptly take literally leading them start climbing on top of a tavern roof while Elizabeth would make her escape.
Rex has tried on numerous occasions to propose to Amanda. Every time, a more urgent matter comes up and distracts him. He only finally managed to succeed during the final battle.
"Lance Williams, the surfer?" is the most common response to anyone hearing his name, regardless of whether they should logically know a thing or two about surfing.
A bit of a Running Gag with Adventure during the final battle is that he kept trying to deliver Pre-Mortem One-Liners to Dr. Rex, but the trope would always be subverted.