While there are 2 known workarounds for this "patent" (1. like MS did require an extra click or 2. create the tags dynamically e.g. with JavaScript) one should read Perry Pei-Yuan Wei (ViolaWWW) comments on that he wrote tmk when the MS vs Eolas case was ongoing. Only available via I-Net Archive at http://web.archive.org/web/20100625180207/http://www.xcf.ber...

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"....My personal experience in this is highlighted as follows. I can fill in the details later, but this will give you a quick idea. In 1991 I started writing the Viola web browser. Starting at this time, on the public world wide web development forum, and to some key players in web technology, I suggested that I will be teaching my viola browser embedded interactive technology. But of course it takes a while to just get the basic text/graphics browser working, before the more advanced embedded-in-page interactivity can be built. In April 1992, I made a released of the viola browser. By December 1992, I had embedded objects working in the Viola browser. We at O'Reilly and Associates gave demos to various people here and there. The best documented demo was in May of 1993 -- We gave a demo and code to SUN Microsystems, of the viola browser showing an interactive three dimensional plotting object (mathmatical equation or 3D models) embedded inside a web page. I started releasing this code around fall of 1993 and early 1994. Eolas filed the patent in November 1994.

Now, as you probably know, Michael Doyle (Eolas's CEO and sole formal employee as I understand it), wrote to the net about his technology and eventually intent to patent this. So of course people (including me) wrote back informing him of prior arts. I'm not a lawyer but as I understand it one is supposed to disclose to the PTO any relevant prior art for the PTO examiner to assess. Doyle and I exchange letters, and I told him about this embedded capability in Viola, gave him a paper on viola, which contains pointers leading to more information including even the viola browser source code. Doyle ends up mentioning the browsers Cello and Mosaic, but interestingly not Viola! Now, Viola came before both Cello and Mosaic, and non of those two other browsers had any kind of embedded interactive capability at the core of the discussions...."
"...Personally, perhaps the top two issues that strikes me as odd, out of many in this case, are as follows.

Firstly, I was not allowed to demonstrate Viola to the jury. It was explained to me that the judge had decided that my demonstration, of the Viola browser from May 1993 showing interactive objects embedded in a web page, would have been too "prejudicial" against Eolas. I was also not allowed to tell the jury that Doyle knew about Viola. This I suppose is understandable but still puzzles me a little and leads to unfortunate effects, as I imagine the Jury ought to know these things. Lets not kid ourselves, everything said in court by both sides were certainly aimed at swaying the jury. But facts are facts, especially relevant ones.

Issue number two has to do with the Defense of the Inequitable Conduct (Judge's ruling on the question of "Did Doyle know about Viola browser, and intentionally not tell the PTO examiner about this prior art"). I felt that this was just surreal, as put into the context of the history of the web and this case. Suffice to say that it's amazing how people will believe whatever they want to believe, even in the face of contrary evidence..."

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I guess the last 2 paragraphs of Perry Pei-Yuan Wei's letter tell it all - there have been substantial issues how the law has been used in this case and how evidence has been excluded in these previous rulings.

It also is interesting to look at other patents Doyle filed.

As always when you want to get a better understanding have a look at the patent's file wrapper at uspto.gov to see the various communications during the process of examining this patent. With that patent, particularly as Eolas claims it was disputed since 1995, one would expect loads of communications back and forward but there is less than with many others that are considered undisputed.