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i'm afraid this isn't extremely helpful, but if you are good at research, you might try this: i remember martha stewart (i know, i know) talking about such natural stains for wood on one of her shows, many years ago.

I've used coffee stain by making it with water and instant coffee. I stained an old chair with it. I've never made it with the real thing, though. As a water based stain, you need to be cautious as it will lift wood grain. Ground walnuts suggests an oil based stain.

A weak reference for coffee as a stain: http://www.woodworking.org/WC/Garchive01/3_27colorants.html

Sounds interesting, but I would love to hear about any effective, non-toxic floor stain. Anyone have suggestions? Are there companies that do this and use non-toxic alternatives?

There is a reference here to walnut hull powder
www.basketpatterns.com/PAGE4.htm

This page gives the recipe, offers email advice & uses a coffeemaker:
www.basketsofjoy.com/faqs.aspx

Remember that water raises the grain, so you will have to sand before sealing, and a light stain may sand off.

This page describes traditional chemical free french polishing, which explains why people don't do it:
www.londonjoiners.com/finishes/finishes.php

This one uses ground walnut shells as an anti slip additive:
www.epoxyproducts.com/b_floor.html

And last but not least are the large number of stains sold at Rockler:
www.rockler.com/product.cfm?page=5341