This morning, the research and development company filed suit against nearly two dozen companies, accusing them of violating two of its patents–U.S. Patent No. 5,838,906, the same one Microsoft allegedly ran afoul of, and No. 7,599,985, an extension of the 906 patent that covers embedded apps using AJAX. Among the companies named in the suit: Adobe (ADBE), Amazon (AMZN), Apple (AAPL), eBay (EBAY), Google (GOOG)–including YouTube–Sun (JAVA) and Yahoo (YHOO).

“All we want is what’s fair,” Eolas Chairman Dr. Michael Doyle said in a statement. “We developed these technologies over 15 years ago and demonstrated them widely, years before the marketplace had heard of interactive applications embedded in Web pages tapping into powerful remote resources. Profiting from someone else’s innovation without payment is fundamentally unfair.”

Sadly, “what’s fair” in this case threatens the very fabric of the Web, as Tim Berners-Lee, the computer scientist credited with inventing the World Wide Web argued back in 2003 when Eolas was pursuing Microsoft (MSFT). “The ’906 patent will cause cascades of incompatibility to ripple through the Web,” Berners-Lee said in an appeal to the U.S. Patent and Trademark Office. “[It] is a substantial setback for global interoperability and the success of the open Web.”

At the time, it seemed the company had no intentions of settling, saying it would rather ship an altered version of Internet Explorer 6 that sidestepped the company’s patent. “We believe we have substantial grounds for reconsideration by the judge,” said Michael Wallent, a general manager in Microsoft’s Windows division. ” … [T]he idea that we would pay more than $630 million ($520.6 million in damages plus $111 million in interest) to get rid of a single mouse click on a small fraction of Web pages is not something that we’re entertaining.”

But after a few more years of pitched battle, Microsoft has apparently softened that stance a bit. The Seattle Post-Intelligencer reports that the two companies have finally resolved their differences. According to a letter to Eolas shareholders from COO Mark Swords, the companies settled the case last Friday.

Terms of the settlement weren’t disclosed. That said, enough money seems to have changed hands to warrant a dividend of between $60 and $72 per share to shareholders.