Like many people mensioned before here, TS3 is very funny, i loved the way Cortez interacted with him self in time paradox.
Another funny one was the begining of RE4 when your with the binoculars looking at el pueblo, danm spanish, they don't know how to talk with out saying "Mierda!".
I also laughed a lot with disgaea in the Power Ranger part, when 2 of them get killed and the red one starts screaming "BLUUUUUUEEEEE!!! YEEELLLOOOOOOOWWW!!".
The radio on gta3 was very funny, I remember one part spcifically, where a mother was talking about her kid beeing so addicted to video games that he was running around the house looking for golden coins, and when he was run over by a truck he screamed "Mommy! Mommy! Where's the reset button?!"
A particular funny and strange thing happend to me when playing OOT on N64, I was riding Epona when suddenly Link start flashing in and out and he disappeared from the top of Epona, the horse kept going but link was nowhere, this was during the big goron sword quest, I was a bit upset