I like the way footnotes are implemented here: Snakes on the Web by Jacob Kaplan-Moss.
(Recorded with byzanz. My gif-fu is nonexistent or I would make it loop, but with a sufficiently long delay at the end to avoid irritation. Now you have to reload the whole page if you missed the animation.)
I'm somewhat ambivalent about the animation effect. On one hand, shiny! On the other hand, hitting tiny clickable areas is not good usability. Still, shiny!
Footnotes are kind of a personal pet-peeve of mine.