The biggest thing is to remember that you're in a place of business. If you're going to take their space, buy something, tip well, and be courteous to the people around you.
A netiquette for coffee shops, I wholeheartedly agree.
I work at coffee shops a lot; I keep sitting there when I can see there are plenty of empty tables - that means my sitting there is a net positive for the Cafe: I might consume more, and often do. And having customers is better than having none, it attracts other people.
If I see that many customers are coming and that I might actually block people from getting a table, I leave.
Only exceptions is Starbucks because its a huge chain and they have always had an official sit as long as you want policy which has worked out very well for them. I am not sure about the actual business trade off but I often end up at Starbucks because I know I can sit there as long as I want - this business might otherwise have gone to independents. I realize though that what works for a large chain might not work for the coffee shop on the corner.
On the other hand I can relate to the concept of doing good by those whom you rely on, a symbiotic relationship and what not. That's a very pro-society thing and I suppose that's respectable.
If you act considerately and don't cause problems (like occupying space when you are not spending) then this is less likely to happen, so there is certainly a degree of self interest.
In turn, they _like_ having me around. I've sold old hardware to one, gotten novel draft feedback from another, and have plans for a weekly anime get-together with another. That, and I even get plenty of free drinks!