Keeping body parts dry when the surroundings are wet is kind of a holy grail, which is to say no one's found it yet.
My own preference is well-ventilated trail runners or light boots (depending on trail conditions) combined with waterproof socks (Sealskinz). It is possible to use something as simple as plastic bread bags in place of waterproof socks, but of course these are more useful as stopgaps than as reliable equipment.
The biggest difficulty with waterproof boots is that once water enters them they do not dry out very quickly or easily, and this includes wetting out from foot sweat. The breathability of WPB materials is never going to be more than a small fraction of the breathability of mesh.
So, unless you know in advance that you will be hiking in the rain all day, the non-WPB boots combined with WPB socks is easily the most versatile approach - in my experience. Edit; I also wear a thin wicking sock inside my sealskinz, which helps keep my foot as dry as is possible for them to be under the circumstances.
Just realize that no solution to this problem is going to be perfect.
Edited by aimless (09/11/10 04:07 PM)
Edit Reason: Additional info.