What math mark-up language is used by the United States Patent Office
in its published patents? For example, Patent Number 6,633,648
contains the equation

S.sub..alpha. =C.sub.w S.sub.w =C.sub.t S.sub.t 

which is a simple equation involving the variables S and C but with
subscripts such as alpha, w, and t.

It is not TeX, Microsoft Word's EQ field, or MathML as far as I can tell.

Download the new ABX MS Word add-on for creating electronic patent
applications from www.uspto.gov in the electronic business center.  It
saves to an XML file.  Perhaps this XML file will give you insignt
into the mark-up language.