The issue published after 9/11 was just exactly what we needed:
Attack on America: Holy Fucking SHIT!
(Alas, I can’t seem to find a direct link to the article)
This valedictory for President Bush got me giggling: The Onion | America's Finest News Source.
And I liked this one, too. Turnabout is fair play!: The Onion | America's Finest News Source.
Our Dumb Century is definately pretty good.
Headlines from the seventies: “Everybody Kung-Fu Fighting” “Carter to Congress: Give Me A 10-20, Good Buddy”
After 9/11 they had a great edition called “HOLY FUCKING SHIT: Attack on America.” Some of the articles I could find are:
God Angrily Clarifies ‘Don’t Kill’ Rule
Hijackers Surprised to Find Selves in Hell
ETA: Beaten by Unintentionally Blank!
Why Do All These Homesexuals Keep Sucking My Cock?
“Ebert victorious.”
After the death of Gene Siskel.
This is pretty good:
This too:
I don’t think that I’ll ever stop finding Johnson & Johnson Introduces ‘Nothing But Tears’ Shampoo To Toughen Up Newborns funny.
One of my favorites is a short one: Neighbors Remember Serial Killer as Serial Killer.
That was priceless. 
I’m forced to admit that my candidate for funniest Onion story ever has already been beaten and whipped into whimpering submission several times in the space of this thread already.
I’ve obviously missed some real classics.
Some of their one liners are great because they let you use your imagination. I could click these for hours
Here’s one to get started
Carbon-Monoxide Detector With Snooze Button Recalled
Fuck Everything, We’re Doing Five Blades is my favorite. And it has come to pass!
I have to admit that this one makes me laugh every time.
When it gets chilly I always think “Time to be rolling out the cold weather whores” - unfortunately not as many people in earshot have ready the article as I thought, according to reaction…
Really only funny for fans of “Lost”, but if you ARE a fan, this is the funniest of all the Onion articles: http://www.theonion.com/content/news/smoke_monster_from_lost_given_own
I always loved this one. I especially loved the fact that a few years after it came out, some idiot fundamentalists got caught trying to pass it off as a real headline from a real newspaper.
On the other hand, this article is cause for grave alarm!
Agreed. The Onion bits that leave me howling with laughter are the ones that leave my brain to supply the missing details, like an electrical spark arcing over a gap in a wire.
I’m sure there are better examples, but here are a couple I could come up with right now:
Real Toy Used As Sex Toy
(from before Steve Irwin’s death) Crocodile Hunter The Same Way In Bed
I always loved the horoscopes.
My favorite was the horoscope “correction” they once published. “Last week’s horoscope was incorrect. The line ‘tall, dark stranger’ should actually have read ‘enraged lowland gorilla’. We apologize for any inconvenience.”
Another article that belongs in the other thread regarding Onion articles that ended up predicting the future. Who’d have imagined that PepsiCo would end up releasing Mountain-Dew-flavor Doritos a while back?