At least 10 times per year I get the call. A wife spends quite a while describing her wonderful husband, then hones in on his "messy man cave." Its always a sore spot. Its ruining her lovely home. So, off I go to work with a man that normally isn't happy about spending his free time organizing. I have even had them give me a check, and drive off. "Do what you can!"
Lets define the term "man cave". Its usually a room inside the house where guys can do as they please with out fear of upsetting any female sensibility about house decor or design. This room could be an office, attic, or basement.
How should you deal with a messy man cave? Well, It depends on the effect is has on the household!
If the man cave functions as an office, and the disorganization is causing problems with daily functions of the home, I would address it. By daily functions, I am talking about bill payment, project management ect.
If the man cave is visible to other areas of the home and can't be shut off, I would address it.
When the man cave is a separate entity, that can be closed off from the other parts of the home, I would leave it alone.