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One of the big challenges Microsoft faces in mobile phones is that developers don’t have the time — or resources — to make new applications for the emerging Windows Phone platform. The software giant is using its checkbook to help jumpstart that ecosystem.

But as it turns out, even that financial incentive doesn’t always work.

As The New York Times reports, the company has been paying creators of popular mobile apps like Foursquare and Cheezburger to move their apps into the Windows Phone universe. Microsoft is also promising advertising and prime placement in the company’s app store.

Last month, Microsoft and Nokia announced that they are investing $23 million into a program called AppCampus to help spur even more app development.

Obviously, as we’ve reported in the past, Microsoft has a long way to go to catch up to its rivals. Developers have created some 70,000 mobile apps for the Windows Phone platform, which may sound like a lot until you realize that Android and Apple’s iOS are in the hundreds of thousands.

And many popular apps, such as Pandora, Redfin and games from Zynga, aren’t available on Windows Phone.

Redfin tells GeekWire was approached by Microsoft about the subsidy program, but the Seattle online real estate company turned Microsoft down.

“We had to focus on the platforms that the vast majority of our customers use to connect with Redfin,” said spokesman Matt Wakefield, adding that there’s still a maintenance cost associated with keeping apps up-to-date.

“There is an opportunity cost here, of course, and right now it just made sense to keep focusing on Android and the iOS apps, for the time being,” he said. Redfin unveiled a new version of its iOS app today.

Redfin’s cross-town rival, Zillow, does have a Windows Phone app and it did receive a subsidy from Microsoft.

Many of the small mobile app developers we talk to on a regular basis say they just aren’t investing resources in Windows Phone, choosing Android or iOS instead. For many, Windows Phone isn’t even part of the conversation until we bring it up.

The subsidies for app developers could help solve those problems, but there’s also the potential for backlash. After all, what does it say to those app developers who actually invested their own resources in developing for Windows Phone, the early adopters? Will everyone now be looking for a handout?

Steve Murch, a former Microsoftie and founder of the popular mobile recipe app BigOven, was an early adopter of Windows Phone, creating an app for the platform in late 2010. Even though Murch wasn’t approached about the subsidy program, he’s glad that he got out in front: BigOven is now the leading recipe app on Windows Phone.

BigOven's Steve Murch

“We’ll continue to invest in Windows Phone since our WinPhone users love it, the platform shows promise with new devices (notably the Nokia partnership) and it shares a great deal of similarity to Windows 8 app development,” Murch tells GeekWire.

And Murch said he won’t feel slighted if Microsoft helps bankroll his rivals.

“I’m supportive of the idea, as I feel confident we’ll continue to have the best app in the cooking category, and a rising OS tide lifts all apps,” he said.

But Murch has some advice for Microsoft, suggesting that they complement the subsidization program with outright acquisition of a portfolio of apps so that they got first, or only, access to the best apps.

“Imagine if the only place you could get Instagram or Draw Something or BigOven were on Windows Phone?”

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