I think it depends on how busy it is. If the place is dead, they'd probably be grateful for you to sit there and make it look more happening for someone who comes in. But during busy time, clogging up table space for three hours on one coffee is probably aggravating.
When I go to a non-chain, if I want to sit for longer than is normal, I just ask them. "I was thinking of having a coffee and hanging out on my laptop for a few hours - is that okay with you?" 90% of shops will say yes if they're not busy, or tell you when the time that that they get busy is. 10% will give a hesitant yes or non-answer, and I'll either only stay a short time or head out from there. Like everything, it depends on the particular situation.
If it gets busy and its been a decent amount of time (30-45m-ish) since my last purchase, I'll just head out.
The exception to this rule is the coffee place in my college's library; there's plenty of seating in the rest of the building. If I'm on a couch there, I tend to stay there until I'm done with whatever I'm working on.
I worked for another corporate coffee company and we never gave any customers a hard time for staying for hours or holding meetings. It was the same philosophy we had for re-doing drink orders no matter what the complaint. Sure, some small fraction take advantage, but for every illegitimate complaint you ferret out by putting up resistance you will irritate at least one paying customer, and that's a customer you lose forever.
The economics might work out differently for an independent coffee shop, but I doubt it. I find it far more likely that many coffee shops are opened by people who aren't that great at business or customer service in the first place and just think starting a coffee shop would be cool.
In sum, spend as much as you like on the products you want, and don't worry about it. If the shop decides you're a drain on the business, it's up to them to ask you to leave, and lose you as a customer forever. That's their calculus to decide, not yours.
I can't possibly imagine eating and drinking enough to justify my presence in a cafe for an entire day.
Each table needs to earn $n each hour to keep the place in business. If you enjoy your neighbourhood café, you should do your part to add to that revenue as much as possible while you enjoy their services.
His biggest complaint/cost/profit issue is the price of milk and how much is used in a latte.
Your comment brought one idea, I know there are white/brown noise samples, and nature sounds that make the atmosphere more ambient. Does anyone know sound samples taken in coffee shops?
On this topic, there's sometimes a really annoying hum where I live. White noise solves it. In summer, I use a box fan. In winter, I used to use this:
cat /dev/urandom > /dev/dsp
And now use this, because it can be set with lower frequencies: http://freshmeat.net/projects/whitenoise/But the best thing is to take a brisk walk in the fresh air, and notice nature. How fortunate to be prompted to do this beneficial thing! (a convenient rationalization that is also absolute truth.)
Do you leave your laptop at the table? Pack the expensive stuff up and and take it with you? Find a pal and ask them to watch your stuff while you go pee?