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What should I use to fill gaps between floorboards?

I have a natural wood floor that I'm sanding to re-varnish, but there are gaps between many of the floorboards, up to 5mm in one or two places. Most wood fillers state they are not suitable for this purpose, so what should I use instead?
I'm also wary of how a filler might respond to the varnish I later apply.
Hugo Slim, February 2009
Save the sawdust from the final sanding and mix it with a 2 part epoxy resin.
This will give a finish that's the same colour as the original boards.
You might need to fill the larger gaps with mastic first if your floor is on joists to stop the epoxy falling through.
Be sure to leave space to apply 5mm of epoxy on top of the mastic so it's flush with the boards.

Big Softy, February 2009