Mogees, a company that wants to give mobile developers more flexibility in how they make money from their applications, is now getting into the app store business too. The Mountain View, Calif. company just told us it has acquired BerryStore, a store for third-party applications on the BlackBerry smartphone.

The terms of the deal were not disclosed, but the two companies seem like a good match for each other — one of BerryStore’s biggest differentiators is the fact that developers can charge as little as 99 cents for an application, while apps in BlackBerry-maker Research in Motion‘s not-yet-opened BlackBerry App World will have to cost at least $2.99 (or be free). That’s an obvious fit with Mogees mission of flexible monetization. BerryStore also allows developers to keep an unusually large cut (80 percent) of the revenue and has also received positive reviews for allowing apps to work across all carriers, rather than selling carrier-specific applications like App World.

This acquisition is the first that pits Mogees in direct competition with the smartphone app stores — previously, it was just trying to offer additional options for paid apps, such as subscription fees, free trials, and virtual goods. This allows Mogees to create a fuller solution encompassing both distribution and billing. The move is particularly smart since a billing solution alone might be threatened if app stores start offering more options themselves — as Apple announced in its plans for verison 3.0 of its iPhone operating system. (Mogees launched its payment platform last fall for the Android and recently added the BlackBerry, but hasn’t announced any plans for the iPhone.)

Mogees has raised an undisclosed amount of angel funding from Ron Conway and other investors.

Update: By the way, BerryStore founder Fred Potter says he won’t be working at Mogees. He also confirmed that he hadn’t raised any venture funding.

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