There are some notable omissions from Linux Magazine's list of the top-20 companies for 2008 (MuleSource, MySQL, etc.), but it's an interesting list because it doesn't read like a standard list of open-source companies. Or, rather, it takes a more expansive, .
Hence, the list includes the usual suspects like Alfresco (correctly reading that Alfresco is a serious threat to Sharepoint's growing dominance), Mozilla, Ubuntu/Canonical, Red Hat, and rPath, but also Google, Yahoo!, and...Microsoft.
Remember: This isn't a list put together by Wired or some publication like that. It's put together by Linux Magazine which has tended to be more grounded in a traditional Linux/open-source approach. Apparently open source is opening up.
Discoslure: I am an employee of Alfresco and an advisor to MuleSource.