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Has to be The Fellowship of the Ring. It's far and away his most ambitious undertaking, and with the way those books are beloved by so many generations, the margin for error was nonexistent. Everybody hoped for the best, but down deep every fan who had seen one awful adaptation after another in the realm of Fantasy, Sci-Fi and comic books knew the chances of failure were enormous. That Peter Jackson pulled it off so brilliantly, satisfying EVERYbody - hardcore fans, newcomers, and those who have never heard of a Hobbit before, it is an amazing accomplishment.
Before The Lord of the Rings, I would have said Heavenly Creatures without hesitation, which is such an inventive and wonderful way to treat a true crime story. After that, I love "Forgotten Silver". It's only about an hour long and made-for-TV, but it holds a special place among mocumentaries and is very well done.
I know there are tons of fans for Bad Taste and Dead Alive, but other than as fun documents of how far he's come and a look at his warped sense of humor, I don't have much use for them myself. It's fun ultra-low budget filmmaking, but that's about it. Meet the Feebles falls likewise in this same category, but it's elevated for me anyway because of the sheer fu*ked-up inventiveness of the idea.
I didn't care much for The Frighteners and thought it could have been/should have been more than it was. They missed on that delicate tone between horror/comedy or comedy/horror, a mix pulled off so well in An American Werewolf in London and Ghostbusters, but rarely duplicated. Those are good special effects, especially considering they were figured out in-house over in New Zealand, and definitely a stepping stone to the visual achievements of The Lord of the Rings. But the overall movie should have been so much better than it is.
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"Film is a disease. When it infects your bloodstream it takes over as the number one hormone. It bosses the enzymes, directs the pineal gland, plays Iago to your psyche. As with heroin, the antidote to Film is more Film." - Frank Capra