Of course, many in the free and open source software community believe that software patents are highly problematic in multiple ways--myself included. But the hope now, at least in the short term, is that Microsoft will prevail in this appeal, making it easier henceforth to challenge bad patents and win. If that happens, we'll all benefit from the increased innovation that will surely result.
A decision is expected in the case in the first half of next year. In the meantime, the EFF plans to file another briefing in support of Microsoft, and supporters of open source software around the world are keeping their fingers crossed.
I never thought I'd say this, but this is one court battle Microsoft really needs to win.