I think there are many interesting reflections around this, but it seems there are several different ways of digging the way forward and clearing the fog.
At least in my personal opinon, if you are interested in entropy reasoning, and want to take it beyond the classical (successful) context of stat mech and chemistry, a very exciting and promising route is by means of information geometry, various "maxium entropy" methods, and bayesian reasoning.
Ariel's papers is pleasant reading
http://www.albany.edu/physics/ariel_caticha.htm
Is some pages which contains various links to the topic of Max Ent methods.
http://www.cscs.umich.edu/~crshalizi/notebooks/max-ent.html
IMO, a deeper usage of entropy should be avoided unless the meaning of entropy is analyzed, and one realizes that the more sensible versions where entropy is relative. Which ultimately leads into information theoretic reasonings on learning.
Then, I think the basic machinery can be applied to many different things.
The above links may not contain anything directly applicable to cosmology, but I think the basic question posed there, should be kept in mind when applying the ideas, because often classical entropy methods are really special cases as they contain a few assumptions, for example uniform priors that are dependent on the representation (model or coordinate system).
/Fredrik