Disadvantages of software Patents
1. Furthering Monopoly
Software patents let companies such as Oracle buy up patents on technology created by others and then launch lawsuit after lawsuit as a way to generate revenue. This is what it means to be a "patent troll," and it's of course motivated by the huge sums that have been awarded by the courts in the past. It also puts the advantage squarely in the hands of the industry's monoliths, which are the ones with deep enough pockets to acquire and assert all that intellectual property.
2. Hindering Innovation
By their very definition, patents reduce the sharing of new ideas. In the software industry--which relies on just that kind of diffusion to spur further innovation--that's particularly destructive. Software patents frequently have very broad or vague boundaries, making it highly unclear where the patented piece of a program begins and ends. Frequently, software patents cover what can be considered the equivalent of a sequence of notes in a piece of music; imagine if that were to happen in the music world!
It has also been historically very difficult for patent offices to judge patent quality, or to realize when a patent application is too broad or covers something trivial.
3. Cost and Time
Patents are extremely expensive, and the examination process takes a very long time. Not only are the costs extremely high to determine if a particular piece of software infringes any issued patents--thereby reducing the funds companies have available to spend on R&D--but the results are highly uncertain, and take a ridiculously long time. Patent applications are often not disclosed until the invention becomes widely used, so developers frequently have no way of knowing if a useful new idea may become patented in the future--potentially after they've begun to use it.
4. Harming the Little Guy
For all of the above