well, you can sell off all iprovements, set all citizens to science(or some speacialty) and cause them to starve. They will slowly die off and once the city is size 3 you can disband it into a settler.
This has no effect on the enemy though. If anything, your empire happiness will decrease, but I found it a good way of keeping my total amount of cities down and making some extra cash.
another cool thing is to bombard a city with cannons or another bombarding unit. You can kill off any units by doing this and then watch the city slowly shrink in size. This does piss off the AI/ Mp players.