The best is new metal. You can cut out a metal plug that's alittle smaller than the hole, then weld it in place.
I've used some of the new POR15 bondo type products, and they rock. Like a cross between bondo and resin. They make a floorboard repair kit like what you want - designed to fill holes in the floor board.
You could also do a combo of these. Weld a larger metal plate behind the hold, then bondo over the outside.