The move puts the W3C firmly on the side of Microsoft, which in August was ordered to pay $520m in damages to Eolas Technologies and the University of California for patent infringement.
In a letter sent to the US Patent and Trademark Office, Tim Berners-Lee, director of the W3C, said the "906" patent, which covers the technology allowing interactive content to be embedded in websites, should be revoked.
Berners-Lee said "prior art" - a legal term referring to technology in existence at the time a patent is applied for - showed that the 906 patent was invalid.
"The object embedding technology has been part of the HTML standard since the early days of the web," he wrote.
"This feature, supposedly covered by the 906 patent, provides critical flexibility to web browsers, and gives users seamless access to important features that extend the browser's capabilities.
"Nearly every web user today relies on plug-in applications that add services such as streaming audio and video, advanced graphics and a variety of special purpose tools."
Although Microsoft is appealing against the ruling, it is also making changes to Internet Explorer that may affect a "large number of existing web pages", the W3C said.
"W3C urges the US Patent and Trademark Office to initiate a re-examination of the 906 patent in order to prevent substantial economic and technical damage to the operation of World Wide Web," Berners-Lee said.
"The impact of this patent will be felt not only by those who are alleged to directly infringe, but all whose web pages and applications rely on the stable, standards-based operation of browsers threatened by this patent."