There are so many from which to choose…Michael Keaton getting cast as Batman…Highlander 2 making it clear that there *could * be more than one…Jar Jar… but for me the collective scream that should have been audible all the way to Antarctica was:
The Sephiroth Fanboys squealing in horror when it was revealed that Lance Bass would provide the voice of their idol in Kingdom Hearts.
It’s a toss-up between:
Midichlorians,
and
Han shot first.
And I wish they’d shut up about them both.
Well, they were dead right about both of them, so…
Add in the revelation in the Doctor Who TV movie that the Doctor is half-human.
And god-allmighty- he kissed a woman!
Did the Trekkies cry blue murder when Kirk died?
My personal howl of outrage…nipples on the Batsuit.
The Scouring of the Shire
or
Tom Bombadil
Take your pick
I still loved the movies, however.
Despitw the fact that he had about 2 lines and delivered them well, of course.
I believe it was N’Sync or the Backstreet boys who were going to appear in Episode 2: Attack of the Clones. Of course, none of the ragin fanboys noted that, in fact, they were going to basically onscreen as anonymous Jedi and get immediately blown away by droids.
I hated that, but it seems like most Whovians have learned to deal. Lungbarrow, the book that elaborates about his family mentioned it. (Available here Personally, I just go with the fanon on this.
Oh, and as for outcries, it wasn’t the biggest, but I really loved the following:
Cite .
You just gotta love Ellison.
He’s a dick. But you gotta love him.
I’d contest that.
The first and third sentences, anyway.
My personal outrage moment was when I heard Nicholas Cage had been cast to play Superman - fortunately, it fell through.
The howl that came up when people found out about Arwen accompanying the Fellowship along on their quest so they could promote the love story.
H.e.a.t.?
Bah! Those all pale in comparision to the hue and cries that went up way back when NBC cancelled Star Trek (TOS). 
I think Ellison’s been proved right, over time. I am curious as to what he’d say about Firefly, mind you, but you can’t really do SF on TV that well. Too darn boring.
Even B5 isn’t really hard SF.
The Rubber Batsuit was a bigger outrage than Keaton, as I recall.
But the biggest fanboy howl? Ever?
Crisis. And Byrne’s Superman. Even more the latter than the former, but it was like adding insult to injury.
I wonder what the howl was like when they heard James Bond was going to be played by a Scotsman!
I agree with:
Nipples on the Batsuit
Greedo shooting first
And will add:
Organic web shooters.
Hal Jordan / Paralax.
Not only was it a howl heard 'round the world, but the cleanup on that has been going on for, what? Over a decade now.
Going back: Arthur Conan Doyle killing off Sherlock Holmes
That was what I meant by H.E.A.T.