Flook, 437 U.S. at 594 ("Our approach to respondent's application is, however, not at all inconsistent with the view that a patent claim must be considered as a whole."); Diehr, 450 U.S. at 188 ("It is inappropriate to dissect the claims into old and new elements and then to ignore the presence of the old elements in the analysis.").
As such, if you claim a DVD (an example of a computer readable medium), when the "claim as a whole" is considered, the DVD is patentable subject matter because you cannot ignore that a DVD is neither a law of nature, natural phenomena, nor abstract idea.
"If the only difference between the alleged invention and the prior art is based on content or information, then the alleged invention isn't really tied to a particular machine."
If you ask one having ordinary skill in the art, they will say that a "general purpose computer" with the DVD (or other computer readable medium) encoded with the instructions for perform a method (i.e., the typical Beauregard language) is measurably different than an identical general purpose computer in which the DVD (or other computer readable medium) does not include the encoded instructions.
There may be a difference "based on content or information," as you allege, but that difference is measurable.
FYI your statement that "the alleged invention isn't really tied to a particular machine" ignores that Beauregard claims are product claims, not method claims. Just because you burn instructions on a DVD doesn't magically convert the DVD from a product into some "abstract method."
From MPEP 2141.02:
In determining the differences between the prior art and the claims, the question under 35 U.S.C. 103 is not whether the differences themselves would have been obvious, but whether the claimed invention as a whole would have been obvious. (underlining under "as a whole" omitted."
Under 35 USC 102, you have to establish that the prior art teaches ALL of the claimed limitations.
Thus, you have to look at the claimed invention AS A WHOLE, which includes ALL of the limitations. A blank DVD is not 102/103 art for the average Beauregard claim for those reasons.
The method steps merely describe the "functionality" imparted by the computer readable medium to the computer. As discussed in MPEP 2173.05(g):
"There is nothing inherently wrong with defining some part of an invention in functional terms. Functional language does not, in and of itself, render a claim improper."
Commenter at Patentlyo.com