I made a good looking dirt-cheap custom cover out of some lightweight waterproof nylon:

Lay the cloth over the the saddle ('wrong' side up) and trace an outline of the edge of the leather (yeah, it's awkward on the sides--err toward too big). Fold it in half to make sure its somewhat symmetrical. Then sketch a 1" border all the way around and cut on that line. Sew a buttonhole 1/2" in from the center of the back edge. Fold the edge over and sew a hem all the way around. With slick waterproof fabric this is going to be sloppy, but don't sweat it because none of it shows. Just make sure there's enough hem to feed a small safety pin through. Clip a safety pin onto a shoelace or some other cord and feed it through the buttonhole, all the way around and back out. Slide both ends through a a 20-cent cord lock and tie a knot.

That's it. Fit it over the saddle nose-first, hem down. Tighten down a bit and then make sure it's under the lip of the saddle all the way around before pulling it snug.

I keep it tucked under the saddle. Also serves as a disguise if you're leaving the bike in a hood where it might attract unwanted attention.