[I]t is rare for the developer and provider of high-tech software in the IT field, which the government is promoting, to be punished for users’ abuse of the program. It appears likely that the ruling will affect future technology development.
This Japanese Mainichi article has more details about the ruling. Apparently, the court didn’t like the fact that Kaneko developed his software while being aware that it was (going to be) used for exchanging copyrighted files. The court further found that Winny “physically and psychologically facilitated copyright infringement” and that “most of the files exchanged on the network were copyrighted.”
Kaneko is expected to appeal against the ruling.