When Phineas, Ferb, and Lawrence go into a tomb to look for treasure and are attacked by cobbler's mallets, Lawrence says, "Cobbler's mallets - why did it have to be cobbler's mallets?!"
When Dubois picks the hedgehog boot and is crushed by a large boot, Phineas remarks, "He chose poorly." just like Indiana Jones had to select the correct Holy Grail from among many cups, visitors to the Bootscrappers' Hall of Secrets must select the correct 1807 Dorcham and Wesley boot scrapper from among many
At the end of Phineas's and Ferb's film, a banner falls to the ground as a Tyrannosaurus Rex growls, which parallels the climactic scene in "Jurassic Park."