Well, if you have years of effort put into something which can be copied easily, as is the case with mechanical inventions, drugs, or cryptography/compression algos (yes I think those actually make sense as patentable), that's one thing. Most software is the opposite -- copying it and applying to your business would often be more effort than inventing your own. So the patent system is exactly backwards for us.
Bruce Schneier has written that patents are useless for cryptography. You can't trust an algorithm until a lot of cryptographers have beaten on it, and they don't bother with patented algorithms. Patenting your algorithm just dooms it to obscurity.
