How to deal with multiple affiliations as an author? From the upcoming autumn on, I will be a tenured full-time professor at a regional university. In addition, I will have a 10% side job at an extramural research institution. And on top of that, I'll be an adjunct professor (only title and right to teach and act as thesis supervisor, no contract nor money) at another university. 

My question is: What is the correct way to deal with these affiliations on potential publications?

The options I see are the following:


On each and every publication, I list all three affiliations. I am not completely comfortable with that, though, as the main draw of being a professor is independence - and in the 10% side job, I am of course not independent. Also, it's possibly questionable whether the other university should receive credit for having me as unpaid adjunct lecturer.
I always list my main affiliation (i.e. the university which pays my main salary), and add the other affiliations when this really applies (i.e. if a work is clearly the result of being affiliated with the respective organization). 


Is there other options? Or anything in between? For my academic image, the combination of all three affiliations is certainly not a bad thing, but I feel putting something on my homepage, in my CV or in a public bio is probably different to assigning work outputs to organizations that pay or don't pay salaries.
I'm professor at a university, which pays my bills, and I'm also affiliated with another institution, without any money involved. I do as in 2: I put always first my university affiliation and second the other affiliation for papers in collaboration.

It should be noted that in the recent past I had to fight with a journal because the copy editor arbitrarily changed the order of affiliations just to compact the list of affiliations.