There are two schools regarding software patents: those that see them as broken beyond repair, and those that see them as salvageable after a complete overhaul.
The Patent Reform Act of 2008 (S.1145) takes the second approach, of overhauling the patent system for the sake of reducing perceived problems with software and business method patents.
Unfortunately, the patent system is unitary, meaning that there is only one law for all fields of invention (save for a few minor exceptions). Its unitary nature especially holds for software, because the software patent is a fiction: the text of a software patent invariably describes a computer on which is loaded software, so there is no difference between a software patent as written and a hardware patent.
Therefore, reforms to accommodate software will affect patents for pharmaceuticals, automobile engines, new materials, and every other technology.
Because "patent trolls" create problems in software (and only software), Congress is considering making it difficult for small inventors in any field to collect damages from patent infringement. Because so many software patents are obvious to a person having ordinary skill in the art, Congress hopes to make examination more stringent for anybody who applies for a patent in any field.
The alternative is to simply eliminate software and business methods from patentability, which would allow traditional fields like pharmaceuticals to continue to make use of the patent system. The system for pharma patents may merit reforms as well, but those reforms should be based on problems with the drug market, not the software market.