I looked through the entire thread, and I'm surprised no one has mentioned this yet:
Getting killed by a horde of cuccos in LoZ:OoT. Seriously, the hero of time can stand up to zombies, giant spiders, ghosts, wolfs, etc. But in the end, he subdue to a bunch of chickens. What's even more ironic is that it was because of Link's act that caused the chickens to go Raving mad. I almost suffered at the hands of these beasts, but I managed to escape just in time.