Its kind of cheating as an entry, but Magnus sent me this and I thought it was great. Not only is it a flash movie that has a plot and is genuinely interesting for more than 5 seconds, it is also a comic fan-boy obsessed reworking of Clerks, with decent approximations of Kevin Smith dialogue, which I'm certain could have been done much worse.
This is probably the best Flash movie I've seen, although I should qualify that a little, since Joe Cartoon and Homestar runner, while amusing, when judged as movies indepently are pretty crappy. So really, there's a lot of room to go, but its an interesting step.
I'm not a particularly big comic fan but the material here isn't too advanced, so most general readers should get the idea of it (although the comicnerds will laugh more often).
I am not that much of a comic nerd. But that is really good. Will pass it on to more.