Option 5, of course :)
I usually manage the workers by hand, occassionally setting one or more of them on special automated assignments, some of which may last the rest of the game:
A - fully automated, Don't use.
Shift-A - like A, except doesn't change previous improvements. Don't use that either.
Shift-I - improve city. Not a bad option for cities that you couldn't care less about, like totally corrupt ones on another continent. Core cities are too important to use this on.
Ctrl-N - trade network. Much to important to use early on. Later on, rarely needed.
Shift-P - clean up pollution. Obviously a good thing, if you have railroads. Use as necessary.
Shift-J - clean up jungle. In mid- to end-game, when the order in which jungles are cleared doesn't matter much, I may set a few workers to do this.
Shift-F - clean up forests. Annoying option. I once spent ages trying to figure out which worker was demolishing my forests on the tundras.
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