Hundreds of thousands of developers know that building apps that rely on the Facebook or Twitter platforms comes at a risk—at any time, the companies can change their access rules or launch a competing feature.

The risk is often worth the built-in audience and data from millions of users. Just look at how Zynga grew. Lately, though, as both Twitter and Facebook strain to bring in more revenue and threaten to tighten their platform rules or alter their features to this end, the perennial uncertainty is worsening. For some startups, the situation is even stalling investments or delaying product plans while they wait to see how the future will shake out.

Twitter, which attracted millions of users in part by throwing open its data to outside developers and spawning more than a million third-party apps, has given developers reason to think it may be changing course.

As a business plan for Twitter emerged, the third-party software that many people still use to access the service or interact with it offsite may threaten its ambitions. This is because it cannot guarantee that those using outside apps will see sponsored tweets or the new expanded news and multimedia posts on its site. In a June blog post, Twitter said it would seek a more “consistent” user experience going forward, leading to speculation that it would soon issue more constraining developer guidelines for many kinds of apps. “Consistent” is the same word Twitter used when it began to make it more difficult for developers to maintain applications that closely replicated the mainstream Twitter experience last year.

This time, Twitter has not yet given additional details, leaving startups and investors wondering about how it might restrict access to its platform. Speculation worsened when Twitter stopped allowing tweets to be posted on LinkedIn and also shut off “friend finding” access to Instagram’s photo-sharing app in recent weeks. The CEO of Flipboard, a company that makes an app that curates social news by integrating with Twitter and other sites, stepped down from Twitter’s board this week, fueling further speculation about a brewing conflict between Twitter and the companies that depend on it.

The uncertainty is already translating into economic damages, says longtime Internet entrepreneur Nova Spivack. His current startup, Bottlenose, is building a way to find popular news by measuring activity on different social networks, including Twitter. “There are a lot of companies that have ground to a halt as people wonder. It’s irresponsible,” he says.

After getting no clarification from Twitter about its plans for developers and hearing the other startups cite this as a reason they are struggling to raise money from investors, Spivack launched a petition yesterday calling on Twitter to “uphold [its] promise of being an open platform,” or, at minimum, make its intentions clear.

A less open Twitter may not bode well for innovation in social networking. “If you can’t pull the data out that you want, it makes the kind of stuff you can do less and less interesting,” says Ed Finkler, a developer who built an open-source Twitter client in 2007 but has stopped work on it, partly because Twitter’s rule change last year made developing the app more difficult for him.

Facebook also seems on course for increased friction with third-party developers and startups, especially as its stock price tumbles and pressure to make money mounts.

Last week the social network caused a stir by apparently playing hardball with one developer whose plans might have threatened its growth strategy. When the social network launched its global App Center this week, technology entrepreneur Dalton Caldwell wrote a damning open letter to CEO Mark Zuckerberg accusing Facebook executives of using intimidation to stop him from creating a similar service. Caldwell is now raising money to build an independent network called App.net (see “A Social Network Free of Ads”).

Somewhat ironically, Google, which has not yet given app developers access to its own social network, Google+, seized an opportunity amid the recent grumbling about Facebook and Twitter to gloat. Senior VP of engineering Vic Gundotra wrote on the company’s blog that Google is holding back giving access until it could ensure its rules would be long-lasting. “We’re being careful because we want to be different. You know, actually respectful of developers who build on our platform. It’s novel. I know,” he wrote.

As for Twitter, Spivack doesn’t actually expect the company will shut down its entire third-party ecosystem, but he worries the company could be on the verge of stifling what made it so innovative in the first place. “It seems like many of these big companies have lost their way. They’ve lost their original passion,” he says. And then, in perhaps the most damning assessment one could make of a still-popular social network, he suggests that this could be Twitter’s “MySpace moment.”