There are 2 sides to any transaction. To value a company requires one to know what that company is worth to the buyer. An open source company that makes negative profits could be worth much more than another one that turns a profit if the former one can give the buyer a competitive advantage.
Jboss for instance is very valuable for a linux platform (red hat and possibly novell) but of much less value to IBM being that websphere is a competing product and has a large mkt share in the mkt.
For open source companies where revenues tend to be softer, than their commercial counterparts the value is tied up in intangibles that matter only when considering the buyer.