Is there a rule of thumb for choosing polygon width?
In Eagle, the "width" parameter associated with a polygon is the width of the stroke used to fill it. A wider stroke will be less able to fill narrow gaps between other conductors. But a stroke that is too narrow will cause the resulting Gerber file to be huge because of the number of strokes required.

The width of the narrowest wire used elsewhere in your design is a good starting point, unless you have huge areas of polygon that need to be filled.