Scott McNealy, during his JaveOne keynote today, made sure everyone knew Sun Microsystems and Microsoft are partners moving forward. With a $2.4 billion check, MS and Sun will be working together for the next 10 years, getting the Liberty Alliance and Passport systems working together, getting LDAP and MS Directory Server to work together for an enterprise single-signon solution, integrating .NET and Java, and other joint ventures.

But even though Sun and MS will be working together, the Redmond relationship isn’t all warm and fuzzy. First, he publicly invited Microsoft to get involved in the Java Community Process.

“Come to class and participate and contribute,” he told the crowd. “This is my open letter.”

Apparently, his private invitation for Microsoft to join the JCP hasn’t worked, and a little public pressure was in order. Second, McNealy took a few digs at Windows. He referred to the Java Deskstop System as an “upgrade” to Windows, then blasted Windows for being a warm, moist and welcoming host for a plethora of computer viruses. Viruses cost companies $300 billion a year, he said.

“Where’s the outrage against viruses? … They’re Microsoft viruses.”

Some other notable remarks from McNealy:

  • Sun will continue running Java.

    “Someone’s gotta be in charge.” And that someone will be Sun in the foreseeable future, apparently.</p>

    • 90% of all web visitors will hit a site running Java.

      “Java is everywhere,” he said. “You can’t get away from it.”</p>

      • Sun is healthy and isn’t going anywhere.

        A little scary that McNealy felt he had to say this. But he pointed out that sales are up and the latest quarter’s numbers that will be announced in a few weeks will reinforce this, he said.</p>

        • has 41,000 members, with 1,000 open-source projects hosted.
          • Project Looking Glass is now open source under the GPL.

            This was announced yesterday, as coming soon. Soon turned out to be today.</p>

            • Legislation to force companies to expense stock options will harm innovation.

              He said everyone with stock options will lose them if companies have to count them as expenses. Tell your representatives in Congress to stop the move toward the requirement for companies to consider options an expense. “We can’t have this world run by accountants,” he said. </ul> Now, I’m off to the technical sessions. I’ll update later today on what was interesting.