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One issue standing in the way of open source applications that even the most vehement supporters can't deny is that of patents.

Even though both IBM and Sun recently released hundreds of their software patents to the open source community in the spirit of promoting innovation, many of the up to 300,000 holders of registered software patents in the U.S. might not feel as magnanimous about the situation.

The threat to open source companies is being perceived as stepping on one of these patents and being taken to court. And, thanks to the vague manner in which patents are typically written and the broad interpretations afforded under U.S. law, the threat is real, according to one open source user.

"Patents are interpreted very broadly," says Ed Bailey, director of IT at the University of Florida's Department of Material Science and Engineering in Gainesville.

This can be particularly vexing for small open source start-ups that may need to defend themselves against patent infringement claims. "They're working on very thin margins" and having to pay legal fees in such a situation could ruin them, says Bailey, who studied law. "It's not something that's going to stop me from using open source, but it's definitely something to be concerned about."