It's worth noting that the 3D Graphics patent was deemed invalid based on the "machine or transformation" test given by the Federal Circuit Court in the Bilski decision. This decision has been appealed to the Supreme Court, who will rule on it next year. The prevailing opinion is that they will make some modifications to the Bilski ruling, since the Supreme Court rarely takes cases and just rubber-stamps the previous rulings.
So, depending on how the Supreme Court ruling on Bilski comes out, the software patent landscape could change significantly in the upcoming months, or stay largely the same.
I'm just glad that the court explicitly said that "nonpracticing patent owners" are distinct from those who would benefit from the use of the patent in manufacturing.
Stating that “we observe that Acceleron is solely a licensing entity, and without enforcement it receives no benefits from its patents.[...]" is a very interesting retort to the standard argument for IP holding companies, that being "A patent is a patent, and it doesn't matter whether the owner is going to use it to produce an item or not."
So, depending on how the Supreme Court ruling on Bilski comes out, the software patent landscape could change significantly in the upcoming months, or stay largely the same.