I would also go with the "most important information at top" view. This is what we have for our Roads symbology - highways at top, residential streets at bottom. I was also taught (by ex boss) to use a Points >> Lines >> Polygons order in general, but have the most important layers at top of legend (i.e. the data that you are displaying at top, withe the above order for the "background" or base map data).
I would agree with OZGeo on the Points >> Lines >> Polygons order (from top to bottom). The layers within each of these groups can then be grouped according to "importance." As to what consitutes more important, I imagine, would depend on what you are trying to show or what is the focus of your map.
As for layers like hydrology and contours, I put the major items below the minor ones. I look at it this way; the major items are the "base" from which the detailed items are derived (at least in the contours and, in some sense, the hydrology). The finer contours and the finer streams can be thought of as subdivisions of the major contours and rivers. These are, in essence, "supported" by the major levels and should probably go above them in the legend.
I also liken it to building a structure. The heavier items go on the bottom. So, the polygons go on the bottom, then come the lines, then the points. Within each category, again, the heavier items should go on the bottom and the lighter - or finer, more detailed - items go above them.