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In conjunction with the Windows Mobile 6.5 launch today, Microsoft’s Windows Marketplace for Mobile went live today, providing software developers a new distribution channel for consumer and business applications running on Windows Mobile.

The marketplace is preloaded on all smart phones running Windows Mobile 6.5. All applications are certified by Microsoft to run on Windows phones and backed by a return policy.

ISVs looking to capitalize on Microsoft’s new distribution venue go through a quick vetting process and pay an annual fee of $99. Unlike Apple’s program, which charges a one-time fee of $99, and Google’s program, which is free, Microsoft charges $99 for each application submitted. Through the end of 2009, Microsoft is running a promotion that allows registered ISVs and individual developers to submit up to five applications without charge.

All marketplace applications go through a “vigorous certification process,” according to Microsoft’s developer portal.  All submitted applications must be Windows Mobile widgets or native and managed applications. It is no big surprise that Java applications are not allowed.

As of today, the marketplace houses 246 free and paid applications that target lifestyle, play, social networking, gaming, and business. Among the free applications available are Facebook, MySpace, Netflix, and Zagat, Guitar Hero World Tour and PAC-MAN. According to a Microsoft spokesperson, today’s debuted catalog represents only 10 percent of the number of registered applications. Windows Phone users can expect a “steady stream of new applications coming from a healthy ISV pipeline.”

According to Microsoft, 753 ISVs worldwide are registered vendors and will be making their applications available through Windows Marketplace. As of today, users in 26 countries will be able to purchase applications via a credit card. Users outside those countries have access only to the free applications.

In November, Microsoft will deliver the second phase of the marketplace with support for WinMo 6.0 and WinMo 6.1. The second phase will enable users to purchase applications directly from their PCs – one of the Marketplace’s biggest differentiator to Google’s app store, Android Market. 

Today’s launch of Windows Marketplace for Mobile coincides with the release of several Windows phones running the revamped Windows Mobile 6.5. Microsoft unveiled Windows phones from HTC, LG, Acer, Samsung and Toshiba.