Just last month, Apple posted a warning to its developers not to cross the line when it came to promoting their apps using outside services. These services often promise to drive apps up the charts, into the ‘top 100′, where they can make significantly more money.

They’re also explicitly against App Store rules, as they employ all kinds of shady practices to get their clients there.

Today, an article in Businessweek points out some difficulties related to keeping the now-massive App Store running well.  One interesting tidbit refers to one such company, Gtekna. The company is run by Chang-Min Pak, a former engineer at Adobe, and he made $2M last year gaming app rankings.

To get into this digital store window, Pak charges $9,000 to $13,000. “We are very good at pushing rankings in a short period of time,” he says. SGN, a game-maker led by Myspace.com co-founder Chris DeWolfe, and Seattle-based Big Fish Games are among the companies that have used the service. (Big Fish spokeswoman Susan Lusty says her company no longer does. SGN did not respond to requests for comment.) Pak says he made more than $2 million last year and used it to buy a house in Palo Alto and a Mercedes for his wife.

The kicker is that no one really knows how Pak, or any of the other companies, actually do it. Pak says he buys ad space on popular sites, but others, like Tapjoy’s Chris Akhavan, is convinced that he uses a network of computer ‘bots to generate downloads from fake accounts. Others think that there are farms of real people out there in China that are getting paid to download apps.

Even after the notice was issued by Apple, Pak says he’s still getting new customers.

The Businessweek article points out some statistics that make this kind of gaming so destructive to the surfacing of good apps. About 63% of the downloads on the App Store come from the Apple leaderboards, says Nielsen and the top apps get some 100K a day, according to Fiksu.

This problem of gaming App Store rankings isn’t going away. It’s becoming a huge problem both for developers hoping to see their apps judged on merit and gaining the top charts naturally and Apple, who needs to maintain an environment of trust for those developers. I talked about this back in February when Apple announced that it had acquired Chomp, the app discovery service.

In short, Apple needs to build a community where issues like App Store rankings, unfair reviews and more can be discussed. The current App Store is too much of a one-way conversation and there is far too little disclosure when it comes to unfair practices. Apple has moved 25 billion apps through its ecosystem, it’s time for the system to mature.

This story has been amended to remove a mention of Big Fish Games, which was not involved in the Daily Show segment.