Actually Bilski as it now stands does allow for the patenting of software, you just have to jump through a few more hoops than you did before, which jeopardizes some applications filed before the decision came down without knowledge of what the new requirements would be. It is possible the Supreme Court could categorically rule out software patents, but it seems unlikely.

The DMCA has been a very important body of law for copyright owners, particularly the movie and music industries. Although reverse engineering of software is fair use (not copyright infringement) when used to discover functionality, the DMCA makes it illegal to circumvent encryption or to make a product that is designed to circumvent such encryption. I could see this potentially being a powerful tool in maintaining trade secret protection for software, although the difficulty of enforcement persists. It may be difficult to prove that your encryption was bypassed, as opposed to a competing product being developed independently.

I do not know whether the DMCA has been an effective tool for the software industry in protecting proprietary software. Copyright infringement is not quite as hot an issue in software as in movies and music. If anyone is familiar with use of the DMCA by software companies, please contact me or leave a comment.