I'd always stop in a system that looked interesting, find a planet or moon, drop out of supercruise nearby and drop speed to zero.
I don't think its necessary to drop out of supercruise. But when I've logged off while in supercruise, I seem to return to the game quite a ways away from where I stopped.
Landing on a planet should be fine too, AFAIK. If this were real life, I'd stop landed as often as possible. That toilet is a lot easier to use with gravity.
I look forward to the day when I can get out of my seat, perhaps power down non essential systems, go to the back of the ship, fix myself a drink, catch up on the Galnet news on the computer monitor in my cabin, and hop into the bed and shut down for the night.