I don't do a lot of micromanagement on the city screen -- telling workers which tiles to work. At the beginning of the game, yes, when it is crucial to keep cities with flood plains from growing too fast or to maximize shield production for a particular wonder. But later in the game, when I have a lot of cities, I get them set up to a comfortable size and just let them go.
After the railroads are done, I use the goto command and send all the slave workers to a tile near my capital. Right-click, fortify all. When some pollution pops up, right-click, wake all. Shift-D several times to send them off to clean up the orange goo. If one group finishes early, they will scurry over to the next orange spot and work on it. When they're all done, use the stack command to bring them back to the assembly point. As walletta notes, this is risky during war time. The craters from bombs or artillery when you're blowing up the enemy's resources are also considered "damage", and so the workers will try to repair that, too. Even in the crossfire!
I will also move my mouse hand to the keyboard and use the arrow keys on the numeric keypad for short unit movements -- to vary the motions of my mouse hand, and reduce the number of clicks.