On the one side of this controversy in its largest sense are those — like Bilski and Warsaw themselves — who argue that patents must be available to encourage innovation in devising new ways to conduct business in the global information-based economy, including encouragement for new ways of digitizing business methods.
On the other side are consumer advocacy groups and free-market devotees who worry that patent monopolies could tie up methods of creative thought processes, including teaching, judging, creative writing, making medical judgments, or picking juries (some current, real examples of claims.
The Bilski decision has already had an impact on potential software and biotech patents, in addition to the obvious limitations on business method patents. The petition[PDF], linked from the site of the law firm which filed the brief, argues that the 'machine-or-transformation' test conflicts with the broad language of the patent statute and with congressional intent. It's entirely within the Supreme Court's discretion to take the case or not, but for now it looks like the issue is far from decided.