I don't know how to give an answer that is much more helpful than Zhen Lin's comment, but I'll try.
Categories are very general things, and programs are very varied things, so there are many, many ways one could "encode" (I would say "describe") a program as a category. As long as you can define a set of objects which are relevant to the program somehow, and a set of morphisms between those objects which are closed under composition (and composition is associative), you've described the program as a category.
The objects could be possible inputs and outputs of the program, and the morphisms could represent the way the program maps inputs to outputs. Or, I suppose the program states could be the objects with the morphisms being the allowable transitions between those states. (The requirement for an identity morphism means that a state would be allowed to transition to itself, which might be a bit odd.)
Yes, once you've described your program as a category, you could define functors between it and other categories (which may be other programs) but there is similarly no "standard" way to do this that I've seen. Which objects and morphisms (and functors) you choose will influence what kinds of further things you can model about your program once you've described it as a category.
(Note that I've talked about describing a program as a category, since that seemed to be what you were asking about, but now I'm not so sure. You could also describe a programming language as a category, in which case your program would simply be one of the objects (or morphisms) in that category.)
Edit: I'd just like to add that if you are talking about describing a program as an object or morphism in a category for a programming language (such as a function in Hask), then the term "encode" sounds even less appropriate. Objects in category theory are quite opaque -- there's no way to examine them except to say things about the morphisms that apply to them.
I should also mention for completeness (though I know very little about it) that any category with sufficient structure supports an internal logic, which may even be as powerful as the lambda calculus (which is Turing-complete); so there is this (very different!) sense in which one may have "programs" with respect to a category.