Valley Girl July 30, 2009, 10:06PM EST

Amazon-Zappos: Not the Usual Silicon Valley M&A

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And Amazon is the only e-commerce company I can think of that's actually still innovating—be it through the Kindle e-reader that's slowly remaking the publishing industry or Amazon's cloud-computing services that are reimagining what it takes to build and run a small company.

A Handful of Similarly Smart Mergers

Here's a case where target-acquirer values are genuinely aligned. Amazon says Zappos will be run as an independent company, and the Zappos founders say they'll stick around. I believe them both.

There aren't many other such exceptions, but I've come up with a few:

• eBay (EBAY) and PayPal: eBay is horrific at acquisitions, but the success of PayPal makes up for the failures of Skype, StumbleUpon, Billpoint, Butterfields, and others the company would rather we forgot. PayPal accounts for one-third of eBay's $27 billion in sales. Just this month, eBay CEO John Donahoe predicted that the company will be bigger than eBay in a few years.

To be sure, many of the best people at PayPal left soon after the acquisition, and you can argue—as I did in this column—that under eBay, PayPal stopped innovating. But the service still works and is growing. That's more than you can say for many tech deals. And sure, to this day, PayPal founders and investors debate whether they sold too soon, but when you consider how much eBay accounted for PayPal's user base and the other big challenges such as fraud and gambling that could be better tackled with eBay on its side, the sale was a no-brainer for both parties.

• Adobe (ADBE) and Macromedia: Adobe dominated the market for desktop creative tools, and Macromedia dominated the market for Web creative tools. The companies had many of the same customers, but the products barely overlapped. As I wrote in BusinessWeek at the time, "They were more like twins separated at birth than competitors."

Culturally, the companies clashed. Adobe, based in San Jose, Calif., had become more process-driven and stodgy, while San Francisco-based Macromedia was hip, loose, and innovative. Macromedia's culture certainly hasn't taken over Adobe, but it did inject some life and creativity into the company. And while it's true that Macromedia CEO Stephen Elop left soon after the deal closed, a lot of the Macromedia crew stayed—most notably Kevin Lynch, chief technology officer of the combined company and the visionary behind the AIR development platform that has been installed more than 200 million times.

• Google and YouTube: This one is tricky, since Google still hasn't proven it can monetize YouTube's mammoth video inventory and monthly views. But even in hindsight, this deal makes sense for both parties.

As impressive as paid search is, it's over 90% of Google's business, and one day the market will slow. Despite dozens of small acquisitions and internal product launches, nothing was coming close to creating a business that could move the needle. And while YouTube was a runaway cultural success, unlike most Web 2.0 companies, it was brutally expensive to run.

Add an uncertain business model and the potential for costly legal battles against studios irate over the distribution of copyrighted material, and you see why selling was the right thing to do at the time. The $1.65 billion price tag turned heads, of course, but that was chump change for a company using as currency a stock price that had just crossed into the $400-a-share range.

Likewise, there's cause for optimism that the Zappos deal will stand out. Hsieh is a wealthy man, having made a minimum of $214 million from the deal and he'll get that whether he stays or goes. The only thing keeping him there, financially speaking, is a paltry sub-$40,000-a-year salary. Here's what Hseih says on the matter. "I, [CFO/COO Alfred Lin, and fellow executive Fred Mossler "have no plans to leave." He adds, "This is about building the Zappos brand, culture, and business even faster than we otherwise would have been able to doing it alone. That's why we negotiated for an all-stock deal instead of going with the all-cash deal that was originally proposed to us."

Lacy has been a business reporter for 10 years, most recently coverhas been a business reporter for 10 years and is currently writing a book on global entrepreneurship. Her first book, Once You're Lucky, Twice You're Good: The Rebirth of Silicon Valley and the Rise of Web 2.0, was published by Gotham Books in May 2008. She also blogs for TechCrunch.