(Updated: Added comments from Glu Mobile, Gameview Studios, W3i and more data about apps that have seen ranking shifts. We’ve also added stories here about Facebook’s strange rise to #1 yesterday and how Apple has started rejecting apps that use offer walls. As of Tuesday, April 19, we’ve also added another story showing that new titles are beginning to bubble back up again on the top free charts.)

It looks like Apple made a number of changes to the app store’s ranking system last week, adding in new weights on top of download numbers to determine top apps, according to conversations we’ve had with a few pay-per-install and mobile advertising networks.

“We’ve been noticing changes in the Top Free rankings for at least three days now,” said Peter Farago, vice president of marketing at Flurry, which serves 80,000 applications with its analytics product. “From our point of view, Apple is absolutely considering more than just downloads, which we believe is the right direction to go in to measure the true popularity of an app.” Other pay-per-install networks tell us they’ve been detecting these changes too.

While it’s too early to tell exactly what the new weights are, a reasonable hypothesis would be that Apple is considering factors such as active usage. But we’ll keep talking to top developers and ad networks to learn more as we go. Apple has not returned repeated requests for comment. Flurry says it has theories, but it’s premature to share them with such a limited set of data.

The changes resulted in a pop for Facebook’s mobile app, which jumped to the #1 position for free apps in the U.S. after having mostly lingered between #10 and #20 for the last year and a half. That app, naturally, has extremely high daily active usage with 39.5 million users opening it every day, according to AppData. Netflix jumped to #19 after being ranked between #30 and 50 for the last month, while Pandora is at #6, up from hovering in the twenties for the last two months.

Glu Mobile, a larger publicly-traded mobile game developer with 50 iPhone titles available in the store, noticed that its game Gun Bros, jumped to #32 on the top free list after being more or less range-bound between #75 and 100. Meanwhile, its top-grossing ranking remained unchanged.

“It looks like it’s daily actives and monthly actives. Basically, how much is the product used? Is it just sitting there on the handset or is it being actively used?” said Mike Breslin, who heads marketing at Glu. “Download numbers can have a lot of duplicity.”

Google, which constantly tweaks its Android Market rankings, may have begun weighting an app’s ratio of daily active users to monthly active users — a measure of stickiness — more heavily in recent weeks, according to teen-focused social network MyYearbook. The company had noticed suspicious ranking fluctuations across its entire portfolio of apps. Google did not comment on this.

The changes are a big deal because Apple app store rankings have to date relied heavily on an app’s download rate. This has allowed an entire cottage industry to flourish. Networks like Flurry, Tapjoy and W3i allow developers to pay for downloads, which bump their apps into the top of the charts where they can get even more downloads from having the extra visibility. If they’re good, they stick at the top of the charts. If they’re bad, they fall quickly.

Many of the top mobile-social game developers buy installs to bring new users in the door, who they can monetize later with in-app purchases of virtual currency.

It’s unclear how these changes will affect these developers and networks. For one, if Apple is weighting active usage and ratings more heavily, then that will incentivize developers to create higher-quality, more engaging apps — which is a good thing. But it may also make user acquisition more unpredictable. It may even make it harder for brand new apps to be discovered because the rankings will favor longstanding apps that already have a large, existing base of users.

The financial fallout on these pay-per-install networks is unclear. W3i, one of the larger cross-promotion networks, said it started to pick up the algorithm changes last weekend, but that two of the company’s larger install campaigns had gone normally and that both apps broke into the Top 25.

“Most of us in the industry are still going to use any meaningful strategy we can to get downloads,” Glu’s Breslin said. “The hardest thing is to get someone to download a game. That real estate is so valuable. But we’re confident that once we get there, users will like our games. Quality is king.”

But other developers said they are in the process of re-evaluating the size of their spend on install networks.

“Now that the picture’s a little different, we’re not really sure how smart it is to be spending a lot of money to gain visibility if we’re not seeing the best return on investment,” said John Hwang, who is vice president of social games at Gameview Studios, a mobile developer that Japan’s DeNA acquired in September. Gameview had used an install campaign to help get a recent title, Tap Jurassic, to 1 million downloads in ten days last month.

The rankings adjustment was also not the only change Apple made to the app store last week. The store now lets consumers browse all the way to #300 for top apps, which will ideally give a boost to apps that are ranked farther down in the charts. Before, users could see the top 50 apps.