Whispers of Google’s social gaming service had gone quiet since Facebook marched to the top of the hill and planted its feet at the front of the social gaming pack. But it might still be alive and in the works.

That, or Google just doesn’t know what the heck to do with games.

Kongregate — a GameStop-owned online site that hosts independently developed flash games — released a mobile app this week that brought most of its flash games to devices running Google’s Android mobile operating system. But the application was pulled from the Android marketplace for violating Google’s terms of service less than a day later.

Google said the Kongregate Arcade app behaved like an app store, violating the non-compete clause in Google’s terms of service agreement, said Jim Greer, Kongregate’s CEO and co-founder. That isn’t exactly how the Kongregate Arcade app works — the flash games are cached inside the Arcade app, not directly downloaded and saved — but the argument makes some sense.

“It does seem like a pretty extreme distortion to call something that plays content in a browser to be the same thing as an application store,” Greer said. “By this definition, we don’t see why apps like the Kindle or other music apps aren’t across the line.”

But the fiasco does seem like another one of Google’s ham-handed attempts to work its way into the gaming space. The Kongregate Arcade fills a nice niche for a constant source of free online games that make money off advertising and the sale of virtual goods. It’s the same niche Facebook struck gold in when it brought Zynga and other companies in to make games. And it’s a space Google has been trying to break into in a number of ways (like investing $100 million in social gaming company Zynga). It’s not quite clear, though, how serious the search giant is based on its executive activity.

Killing Kongregate’s application leaves the door wide open for Google to step in and take over that niche with its own version of a mobile game marketplace. It’s also a very Apple-esque move for Google, which has traditionally been seen as a much more open development partner that caters to the independent crowd. It’s pretty out of character for the search giant, which has allowed quite a few shady apps into the marketplace. That was one of the reasons Kongregate decided to work with Android originally, Greer said.

“It’s weird to me that at the same time Apple is becoming more transparent and more open about their app store policies Google would be kind of shutting down on games,” he said.

There hasn’t been any additional contact from Google as to whether the Kongregate app will reappear on the Android marketplace, Greer said. It’s been nearly a full day since the site last spoke with Google, and Greer said he doesn’t necessarily have very high expectations at this point. The application is probably being blocked at a lower level of the approval process where it isn’t fully understood, he said.

The Kongregate Arcade was one way to bring a huge swath of Kongregate’s 13 million gamers to devices running Android. Most of the engineers Kongregate spoke with were really enthused by the application for that exact reason, Greer said. It does seem like a bit of a no-brainer to bring the app onto the marketplace to compete with Apple, which has become a bit of a powerhouse in the mobile gaming space. But this could also be a case of the left arm not really communicating with the right arm, as Google’s Android segment is traditionally blissfully unaware of the rest of Google’s interior workings.

Or maybe Google Games is still in the works and Google is keeping this one uncharacteristically close to the chest. The whole deal does reek of the same kind of muscle Apple has traditionally flexed when pulling applications from the App Store to stave off competition. By contrast, Apple has allowed an app from iSwifter, which brings a limited number of Flash games into its portal-like app on the iPad.

For the time being, GameStop has decided to go ahead with marketing the application regardless of whether or not it’s on the Android Marketplace. The app is featured on the GameStop website and will be pitched in its brick-and-mortar stores across the country. Kongregate is also launching the app on GetJar, a third-party marketplace for Android applications. Android users can also directly download the app from the company’s website.