"Funny Aneurysm" Moment: One episode had Double Trouble stealing the World Trade Center. Fast forward a decade later...
Double Trouble also stole the famous replica of the HMS Bounty, since lost to Hurricane Sandy.
In the second round of the episode "White Out", a contestant picks Baldy Mountain and Rockapella says, "Greg's been there!" Greg then jokes that this will be Rockapella's last year on the show. In fact, this was from the last season before World changed to Time, so it really was Rockapella's last year on the show.
Top Grunge stole the entire rhinoceros population. Now one subspecies of black rhino is extinct.
Genius Bonus: Rockapella's flourishes during the second round often got rather creative in order to stay on the standard rhythm. An episode featuring a looted railway used "finagled funicular!" and one about kidnapped whales included "sedated cetaceans!"
Mythology Gag: The two-note, "wrong answer" buzzer from the bonus round sounds quite similar to a sound effect from the 1989 version of the Where in Time is Carmen Sandiego computer game, which plays whenever you click on something that cannot be interacted with. Whether this was intentional or merely a coincidence is unknown.
Squick: At least a few episodes had the Chief somehow grow an extra face to try to help with searching for Carmen before Greg convinces her to make the prize a trip to anywhere in the lower forty eight U.S. States (or North America depending on which season you're watching.) There was also one episode where the Chief's head POPPED OFF and the reason she called Greg into her office was to help her screw her head back on (while still being able to talk somehow...). Could also count as Nightmare Fuel if you don't know that it's all special effects and/or try to consider how that could have happened.