The business world scoffed when venture capital firm Kleiner Perkins Caufield & Byers announced the iFund, its $100 million pool to invest in startups creating apps for Apple (NASDAQ: AAPL) iPhone App Store, in early 2008. The iPhone and iPod Touch, both barely half a year old at the time, were sales successes but the App Store itself was still an unproven commodity. Downloads were frequent even at that early stage, but it was doubtful that anyone was making any money. How would software developers and video game makers distinguish themselves in an outlet flooded with dice-rolling simulators, gyroscope-driven beer pouring games, and fart apps? How would they convince iPhone owners to spend $9.99 on an app when there were free ones listed on the very same page?

Kleiner Perkins is scoffing now, at the lack of foresight in the investment world two and a half years ago. Ngmoco, the independent iPhone game company behind early App Store hits like Rolando, received $10 million from the iFund in 2008. This week, Ngmoco was purchased by Japanese e-commerce and mobile portal DeNA Co. for a cool $400 million. Since that initial $10 million investment left Kleiner Perkins with more than 25% of the ownership in Ngmoco, that means it will be getting back ten times its initial investment with the earnout.  Kleiner Perkins’ reward of more than $100 million for banking on the App Store proves it: the age of the app has finally arrived.

Or has it? Ngmoco’s business has been based almost entirely on Apple’s line of mobile devices, its success owed to sales through the App Store where developers and publishers alike are free to name their own price. Even though Apple takes 30% of each sale, it’s been developers’ freedom to dictate price that has made iPhone apps the commodity they are today. But with competing platforms — particularly Google’s (NASDAQ: GOOG) Android App Market — that offer the same sales opportunities as Apple’s outlet (Google also takes a 30% cut of each sale) on the rise, will app developers find themselves spread too thin? Or does this just mean that they’ll find greater opportunity with the expanded audience?

Come 2011, four major  app marketplaces will compete across the smartphone market. Apple’s storefront is well established at this point, but Google is preparing for a massive influx of new users this fall. Sony Ericsson (NYSE: SNE, NASDAQ: ERIC) is expected to report 12 million Android-equipped smartphone sales for the quarter ending in September. That’s in addition to the doubled third-quarter profits HTC Corp. reported thanks to the strong sales of Android phones. Both Google and Apple will see new competition from Microsoft’s (NASDAQ: MSFT) Windows Phone 7 app storefront, whose games segment (the leader in app sales across all platforms) will be bolstered by the company’s familiar and successful Xbox Live branding and publisher support from companies like Electronic Arts (NASDAQ: ERTS). Investors shouldn’t count out the Nokia’s (NYSE: NOK) Ovi app store, which is getting new support from the recently launched, Nokia-backed Symbianˆ3 operating system and a contest funded by AT&T (NYSE: T) to fuel new app development for the platform. This isn’t to mention the app stores offering unique products on disparate platforms like the tablet PC section (the Apple iPad App Store) and Google’s ever-expanding network of services (the announced Google TV app store).

Two scenarios can emerge from the new competitive landscape. App developers — independents like Ngmoco, major game publishers like Activision Blizzard (NASDAQ: ATVI), and general app developers like Occipital (which recently sold its  RedLaser app to eBay (NASDAQ: EBAY) )– will foster a healthy cross-platform strategy and serve all audiences across these major platforms allowing for growth and, ultimately, see valuation akin to Ngmoco. It’s very possible that this scenario will play out over the next twelve months given the experience gleaned from three years of development and experimentation in Apple’s storefront. There is an alternative, however. The introduction of new audiences across multiple platforms will both cause a reduction in general app quality due to a need to serve differing hardware, leading to diminished app sales. There may also be a push on the part of the storefront holders themselves to incentivize exclusive development, which will benefit major software companies like ATVI that have the resources to devote to a sole mobile platform, but which could hurt developing companies, preventing them from becoming the next Ngmoco.

This all depends on how well these competing platforms perform over the next twelve months. At this point, Apple and Google’s popularity and momentum might drown Nokia’s Ovi store before it can grow further in North America while Windows Phone 7 might not make an impact of any kind, sending Microsoft back to the drawing board. Right now, investors looking to profit on the emerging app market would be wise to look for companies not popping up in the Apple or Google top ten but that are rising in the top 100. Also, look to companies like Retrevo.com that  are building unique apps for new platforms. Retrevo has just announced plans to develop a unique electronics shopping app, RetrevoQ, for the Windows Phone 7 launch. It isn’t possible yet to predict the next Ngmoco, but it would be wise to learn from Kleiner’s $100 million lesson.

As of this writing, Anthony Agnello did not own a position in any of the stocks named here.

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