Hilarious in Hindsight: During the Grand Prize Disney World episode from 2007, Tom Bergeron joked that his dog was so smart that he had his own blog. This was several years before Disney Channel debuted a show with that very premise.
Nausea Fuel: The Bergeron-era segments "The Naughty Files" and "A Moment of Ewwwww!" specifically showcase grosser clips than the producers were allowed to show before. Snot and vomit gags (usually via babies) have popped up elsewhere as well.
One $10,000 winner featured a decapitated fish head on a plate in a sushi restaurant. It was still moving.
Nightmare Fuel: The Vin di Bona Productions Vanity Plate at the end of the show, up until 2008, had a synth jingle that tried to sound cheerful but ended up sounding creepy. It was thankfully redone in 2008, albeit at the cost of now sounding a tad generic.
Replacement Scrappy and Seasonal Rot: The Fuentes/Fugelsang era is often considered the show's nadir, and rarely sees reruns. On the other hand, the Bergeron era is often considered at least as good as, if not better than, the original Saget episodes. Only time will tell if Alfonso Ribeiro will fall victim to this once his episodes start airing.
Bob Saget said in an AMA interview once that this is one of the reasons why he quit hosting the show in the first place. As the Internet was becoming popular, people were finding more websites (even before YouTube) for uploading funny home videos. He felt the show had become pointless and he honestly didn't think the show would last much longer after he left.
Suspiciously Similar Song: When the theme was overhauled to the ska-era remix used in the Fuentes/Fugelsang and Bergeron versions, it sounded a lot like "The Impression That I Get" by The Mighty Mighty Bosstones.
You can also apply this to dogs. A lot of this is likely because the studio audience has the final vote, and it's usually filled with either grandparents or young parents. The parents are more likely to find cute videos funny.
Tearjerker: One $10,000 winner filmed her son bawling his eyes out after he accidentally stole a cup from a restaurant. Hearing him plead with her not to report him to the police is just heart-wrenching.