Our new Montana house has lots of windows. The yard has lots of deer, turkeys and other wildlife roaming through it. Not a good combination when you have dogs who like to jump up, look out the windows, and bark at what they see.
So we "armored" our living room window ledges, knowing full well we wouldn't be able to keep dogs from leaving claw marks in wood sills. The ledges are covered in slate tile. We had Gene Carner, consummate stone mason from Yakima, come up to lay them down.
If you didn't want to use slate, you could cover your ledges with virtually any type of ceramic tile, stone, or even a cultured marble. These impervious ledges will look nice and protect your window sills from all sorts of other problems, like drinking glass rings, or drips from a plant you've just watered.