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.”