Ok, so the best way to do this would be to do it with particles, or get crafty with some animated deforming geometry and projected textures.

Taking a nurbs cylinder, dividing it many times along it's height, putting it into a lattice that's deformed to the shape of a sand timer, animating the translation of the "sand" in Y into the lattice, then projecting a sand texture onto the object should get you started. Then, it's the same process for the bottom, where the sand is collecting.