Even though there might be a big chance to win the battle in court, the cost of lawyers will be so high that the company probably wins by default.
Until recently this idea could have been put off as fantasy. The battle that SCO started shows it's real. And software patents will give a company plenty of chances to start a legal battle, because the legal stuff involved is much more complicated than for copyrights. You can find an interesting article that connects the SCO case and software patents here.
Companies can and will use software patents in an unpleasant way, because they have money to pay lawyers while open-source software developers don't. Small companies with a tight budget are also likely to suffer.
The use of software patents to protect the investments that a company made in their software is very small. The misuse will be very big, also because patents can be very vague. There is a big difference with patents on inventions of other nature, such as mechanical, because software can be protected by copyright. And a software invention usually doesn't require big investments. You can think of ten items to patent in an hour (believe me, I have done it). Applying for a patent is just a matter of paying a patent attorney.
The European Governement is going to vote on Software Patents on September 24th. September 17th there will be a conference in Brussels. Read about other actions here.
More information about software patents on this page