Speaking of Penny, the fact that she's not only not afraid of Brutus and Nero (unlike the adult Snoops), but is able to keep her cool even when Medusa is pointing a gun at her. This little girl has guts.
Any time Bernard decides it's time to get dangerous. For example, in the sequel, Bernard tamed a razorback boar by grabbing it by the tusks, flipping it over and giving it a Death Glare.
The end of Down Under, where he gets to be the hero.
The Gondor Calls for Aid relay sequence near the beginning of Down Under, with the message being passed along from one unnamed character to another until it finally reaches the Rescue Aid Society.
Just getting to see the sheer number of RAS outposts, and how different they all are; from a jury-rigged console in the Outback to the remnants of a crashed plane in the Marshall Islands, from there to a high-tech listening post in Hawaii, which the RAS has apparently hacked into... and from there, though we don't see the posts themselves, it jumps from San Francisco to Denver to Chicago to D.C. before finally arriving in New York. This really is a well-run, worldwide organization.
Meta one for Down Under; the fact that though there may be other sequels produced by Disney for its many features, this was the only one to be formally included into the canon, and in spite of only really reaching Cult Classic status, it earned that spot.