The search giant climbed from second place last year to take the crown due to its ability to make money and its lack of competition.
"Less cuddly but more profitable than ever, the monster from Mountain View has rivals but no peers," the magazine said.
Apple was rewarded for its successes with iPod and iTunes, and for bundling the iLife creativity suite with new machines, but it wasn't enough in the eyes of the judges to stop it sinking to second place.
To compile the list, the magazine looked at companies that excelled in their field and were actively exploring new ideas.
"To land a spot on our annual Wired 40 list a business also needs the x-factor, a hunger for new ideas and an impatience to put them into practice," said the magazine.
Microsoft was just holding on at 36, eight places lower than last year. "The desktop operating system goldmine won't last for ever. What's next?" the magazine asked.
Dell was ditched owing to consistent cost reductions which have left it with nothing to cut, while Vodafone was given the boot for messing up next-generation 3G services and having to sell its assets just to stay afloat.
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