At first glance, Twitter’s new alliances with Google and Microsoft benefit just about everyone with a stake in the wildly successful micro-blogging service. The three-and-a-half-year-old company announced on October 21 that it had landed separate deals allowing Google and the Microsoft Bing search engine to crawl through its site. That means money for Twitter’s founders and investors, who until now hadn’t generated any revenue. While the financial details of the agreements weren’t made public, industry sources familiar with the deals say both search engines are paying flat fees for the privilege.

Google and Microsoft get the chance to mine the wealth of data—keywords, trends, links—rising and falling across Twitter in real time, a boon for both companies’ advertising networks. And Twitter’s 50 million users, who send messages that are up to 140 characters long, can now better monitor the company they’re keeping and tweet appropriately.

Yet for a large number of companies that have ridden the wave of Twitter’s meteoric success—especially sites that aggregate and parse data—the search-engine deals, as well as other soon-to-be-announced revenue-generating plans, may spell trouble. Early in its ascension, developers freely accessed Twitter’s application programming interface, or API, to create successful mobile, desktop, and Web-based Twitter applications that generated audience share, some profits, and possible investor interest.

The API allows outside developers to create software programs that can freely interact with Twitter’s main program. Companies like Echofon (formerly Twitterfon), an iPhone and iTouch mobile app, TweetDeck, the most popular desktop social-network aggregator, and Twitturly, a site that tracks the most popular URLs being tweeted in real time, have all found a modicum of success by swimming in Twitter’s wake.

However, these companies, born of Twitter’s technology, are creating applications that Twitter itself could easily build. Twitter-based startups “are like the pilot fish that swim along cleaning sharks' teeth,” says Dan Olds, an analyst with the Gabriel Consulting Group, a tech-company consulting firm. “They do so at their peril.” While three-year-old Twitter may be short on revenue, it has plenty of capital to work with. In September, it raised $100 million from Insight Venture Partners, T. Rowe Price, and current Twitter backers Spark Capital and Institutional Venture Partners, according to the New York Times. The deal values Twitter at $1 billion. The Times said Twitter had previously raised $55 million, but saved more than half for a war chest to fund its race with Facebook, which is shooting for 1 billion users around the world.

By partnering with Google and Bing, Twitter may have opened the door for one or both of the behemoths to try their hand at Twitter killer apps. Twitter is also expected to launch commercial accounts where businesses would pay for an analytics dashboard allowing them to better track tweet viewership, as well as an API to allow third parties to interact with the new platform.

It isn’t clear whether Twitter’s agreements with Google and Microsoft restrict their ability to develop Twitter applications in any way. Twitter wasn’t available for comment.

Twitter developers aren’t taking any chances, though. They are rushing to diversify their businesses so that they can stand on their own.

Several developers including Joe Langevin, creator and founder of the soon-to-be-unveiled Twitter news feed aggregator Insttant.com, and Joel Strellner, founder of the Sacramento, California-based Twitturly, a site that tracks the most popular URLs being tweeted in real time, believe Twitter creators Biz Stone, Jack Dorsey, and Evan Williams wouldn’t betray the development community which has helped push the micro-blogging site’s growth.

“I have a pretty good feeling they won’t do that,” Strellner says. “They have this tightrope they have to balance on so as not to alienate the programmers and developers who’ve supported them.”

Still, Strellner admits the search engine deal took him by surprise. He sees the potential for competition from Twitter and its new partners, but diversification was always part of his company’s plans.

What began as a side project for the 27-year-old Strellner back in 2008 took on a life of its own. Strellner had founded the B-to-B Web analysis company URLtrends in 2004 to help businesses track their search-engine rankings. When Twitter arrived, he found it difficult to navigate. “I just started messing around with the Twitter API,” Strellner says. “There was no easy way to determine what links were popular on Twitter.”

So he created Twitturly. Following its launch, Strellner went on a brief vacation only to return home to find TechCrunch had reviewed the site. In the interim, more than 8,000 people had begun using it. By February of this year, Twitturly was ranked in the top-10 Twitter applications on the Internet based on a survey of traffic data culled by the Web-analysis company Compete.

“You do need to diversify,” Strellner says. “I believe there are too many free Twitter applications. If everyone is doing it for free, then nobody is making any money and companies will start folding.”