A blink-and-you'll miss it scene from AMV Hell 5 toes the line between hilarious and a little disturbing.
No link to an individual clip, but in AMV Hell 5 there's a blink-and-you'll-miss-it scene from Naruto where a ninja sinks into a puddle... with the sound bit "I'M MELTIIIIING!" in the background. Hilarious, because if you get it you are probably one of the five people who remember what game that's from without looking at the credits.
That part in I think it was AMV Hell 4 where the famous lines from Troll 2 (They're eating her! etc.) actually fit on one of the holy-crap-I-think-I-just-wet-myself scariest scenes of Neon Genesis Evangelion. The scene? The mass-produced EVAs are ripping apart EVA Unit-02. Cut to Shinji, screaming THEY'RE EATING HER! AND THEN THEY'RE GOING TO EAT ME! OH MY GOOOOOOOOD!
If unofficial ones count, AMV Heck has a brilliant rendition of the infamous toothpick scene from Neon Genesis Evangelion set to the Doo Wop's "Peanut Butter Song".