Except for the few patent holders and Accenture, the tax strategy business community has been largely anti-patent – going so far as to lobby congress to introduce legislation to create a specific exception that would block enforcement of those patents.
In Bilski, the Federal Circuit refused to categorically exclude any particular fields of business or technology from the scope of patent protection. The court specifically mentioned software and business methods as still patentable. Presumably, tax strategies are still patentable as well. The closest the court came to creating an exclusion is for purely 'mental' processes – where each step of the process could be performed in the human mind.
Rather than an approach focusing on specific exclusions, the court applied the machine-or-transformation rule: A process is patent eligible under §101 if "(1) it is tied to a particular machine or apparatus, or (2) it transforms a particular article into a different state of things." Bilski's claim was not patentable as a mental process. Additionally the Bilski claim failed the machine-or-transformation test because it was (1) not tied to any machine and (2) the alleged transformations in Bilski were not sufficient because they did not transform "physical objects or substances" nor did the transform articles "representative of physical objects or substances." Notably, transformation of "legal obligations or relationships, business risks, or other such abstractions" do not qualify as 'transformations' under the new test. The Federal Circuit left the State Street patent hanging – we know the test used in State Street was wrong, but we don't know whether the claimed invention would be patentable under the new test.
Going forward, tax strategies (and business methods generally) that necessarily need computer assistance will be able to obtain protection by including sufficient recitation of ties to "particular machines." Practically, the links should be tied to particular portions of the computer to ensure that the tied machine is "particular" enough. On the transformation side, it is unclear whether the transformation of money will be considered sufficiently "representative of physical objects or substances."