Microsoft will introduce an application store with its newest version of Windows Mobile software, it planned to announce at Mobile World Congress, where it also was to formally open a limited beta for its My Phone data backup offering.

Windows Marketplace for Mobile will come with Windows Mobile 6.5, the newest version of the operating system, and will give users access to thousands of applications, said Scott Rockfeld, group product manager for Windows Mobile. Microsoft also introduced Windows Mobile 6.5 at MWC on Monday, saying the software should become available on phones early in the second half of the year.

While applications stores have been around for some time, Apple’s easy-to-use App Store, accessible from the iPhone, popularized the idea of buying and downloading mobile applications. Now, independent companies, operators and mobile phone makers are building stores that are accessible from handsets and that offer wireless downloads.

Nokia also planned to announce at MWC a new application store that will carry content and programs for users of its phones that run the S60 and S40 operating systems.

Offering an applications store is “table stakes” these days, said Sean Ryan, an analyst at IDC. However, Microsoft hasn’t disclosed a lot of details about its store, such as how easy it will be to use. “So there are still a lot of factors out there. But as a concept it’s a good thing and something they need to do,” he said.

While Windows Mobile phones come in many different form factors, Microsoft offers developers a module they can use to ensure their applications work across all the phones, Rockfeld said. That means most applications in the store should work on most phones.

He sought to minimize the potential conflict between Microsoft and its device-maker customers and operator partners, some of which may also be building application stores. “This isn’t the end-all be-all,” Rockfeld said. “Handango will be there, mobile operators will have their stores. We’re not forcing anyone to make the decision to come to us.”

In addition to the Handango mobile application Web site, PocketGear launched a store for Windows Mobile applications last week. PocketGear also runs a store for Palm applications.

Microsoft has already begun doing outreach to the developer community to let them know how the store works and how they can get their applications into it, Rockfeld said.

Another new service that Microsoft will offer and that the company planned to discuss at MWC isMy Phone. Details about the mobile backup service leaked out in early February. It is now available in a limited invitation-only beta, Rockfeld said.

My Phone will be built into Windows Mobile 6.5 phones and will be downloadable to users of versions 6.0 and 6.1, he said. The service backs up calendar items, contacts, tasks, texts, photos, videos, music, documents and anything on storage cards, to the Web.

Users can set the service to automatically back up phone data once a day. They can also store photos, for example, on My Phone online and later restore those photos to the phone.

My Phone only comes with 200MB of storage space and IDC’s Ryan wasn’t clear on the market need for the service. “The idea of a smartphone is everything is backed up on the PC too, so I don’t fully understand it,” he said. “Maybe for people who don’t want to or don’t know how to back up on a PC might find this more intuitive.”

Rockfeld said My Phone will be valuable for people who lose their phones or who want to upgrade their device but worry about the hassle of transferring all their data to a new phone.

The service is different from Apple’s Mobile Me, said Rockfeld. “Mobile Me from Apple is really about PIM [personal information manager] synching,” he said. Microsoft figures it has sync covered with Exchange, which syncs e-mail, calendar and contacts with Windows Mobile devices.

He also differentiates between My Phone and Mesh, another Microsoft offering. Mesh is more about syncing items from specified folders and sharing that data among multiple PCs and phones. “My Phone is truly a backup and restore service,” he said. “Will these things work more closely together in the future? It makes sense.”

The My Phone service is based on technology Microsoft acquired along with MobiComp in June last year.

Microsoft also announced at MWC that as part of a new contract LG Electronics will make Windows Mobile its primary, although not exclusive, mobile-phone software platform for the next four years. LG plans to launch 50 new Windows Mobile phones, including 25 in 2012, as part of the agreement, Rockfeld said.

Samsung unveiled the Mobile Applications Marketplace, a storefront purposed with peddling Samsung-friendly Windows Mobile and S60 applications to consumers while making developers some more cash than they otherwise might. It’s an admirable idea at face value - but is it the beginning of a terrible trend?

Centralized application stores are nothing new - third parties and carriers have been providing places to purchase mobile software for ages. After the Apple App Store began reporting monumental numbers, however, there was a significant shift; suddenly, those responsible with making the handsets tick wanted to be the ones vending the wares. Google launched the Android Market. RIM announced the BlackBerry Application Center. Palm will be debuting the webOS App Catalog with the Pre. What do Apple, Google, RIM, and Palm have in common that Samsung lacks? They control the platform for which they’re selling applications.

If you’re looking to start an application outlet, you need to be at the reins of the platform; if you don’t, you’re further segmenting an already messy market. With Samsung launching their own boutique, others will likely follow; suddenly we’ve got all sorts of manufacturers all peddling the exact (or nearly exact) same junk in a different way. Some might have an on-device store, while others rely on a web-only storefront - all of which would are likely to have completely different interface. Developers who choose to offer their goods through multiple outlets will need to maintain each one individually, monitoring sales and collecting revenue from each individually. Consumers never get the native, unified experience that makes the App Store so enticing. It’s a step in an entirely wrong direction.

That’s not to say that the device makers couldn’t make things better, however. In fact, they’d have to be the ones to do it - but they’d have to work together. Nokia has been surprisingly mum on the S60 app store topic, and Microsoft’s nose is split between the Windows Mobile 6.5 and 7 grindstones right now - so those two are unlikely to have a fix-all solution for the current iterations of their platform any time soon. Thus, responsibility falls to those pushing the devices off the line. If you’re going to get knee-deep in app sales, guys, you need to form an alliance. One store, one common interface, one thing to pitch to consumers as the place to go.

Should it happen? Certainly. Will it? Of course not. Every company involved is a direct competitor with the rest. By the time they worked out agreeable terms and managed to get it onto devices, Windows Mobile 7 (which will include SkyMarket, purported to be Microsoft’s official rebuttal) will have launched and penetrated enough of the market that developers likely wouldn’t be interested anymore. Oh well.