For example, if something like a method of Agile programming practices were singularly developed before they were popularly used, could a company have patented the 'system' including the parts that describe human interaction dynamics such as pair programming?
Where is the line drawn on a software development method or process being patentable?
From my experience as a software developer I don't see how something like agile can be patented and if it was patented how that could be enforced. Any money you would make from that would likely be more in the form of selling publications and certifications. So that falls more in the copyright and trademark arenas.
The Bilski decision is probably the one most relevant to this question. Unfortunately, the answer is that nobody really knows.
In the Bilski decision, the Court of Appeals for the Federal Circuit ruled that to qualify as a patentable method (rather than an unpatentable abstract idea), the invention had to involve either a specific machine, or a transformation of matter (e.g., mixing chemicals).
The Supreme court upheld the decision (i.e., rejected the patent in question as invalid), but specifically rejected the "machine or transformation" test that the CAFC had created. At the same time, they do fairly directly say that although the machine or transformation test cannot be used as the sole rule, that it is a useful guideline.
I'd take that to mean that if the invention does involve a specific machine or a transformation of matter, it almost certainly is patentable. Otherwise, it may still be patentable, but to do so you're going to have to convince the PTO (and quite possibly courts) that it really is not an abstract idea.
As an aside that's somewhat relevant here, earlier rulings have established that just "computer" probably doesn't qualify as a specific machine, but "digital computer" probably does.
these types of things would most likely not be patentable under 101. the law and judicial exceptions to 101 are rather complex (and nonsensical at times) but in general, a good rule of thumb is that an "abstract" process isn't patentable. often, in practice the patent office will not issue patents that can be done "solely" in a persons mind.
that being said, you could probably patent a tool for implementing agile practices et al. (e.g., aspects of cucumber, BDD, or what have you). obviously this can get pretty close to the actual human steps and there are a ton of patents related to software development, but most deal with the actual software itself.
