The quickest wood filler to use, that will match the material you are using is to mix wood glue with sawdust from your cuttings. Since you want water base filler, use a water base glue. Remember one thing about wiping up excess glue...if the wood is unfinished, try not to smear the excess glue. Otherwise you will end up with the stain being absorbed at a different rate when the glue was smeared. The best solution is always to stain the wood first and preferably, to apply at least one coat of finish. That way the wood will have no chance to get onto the wood surface.

Woodwork Safely,
Jim Barry
www.woodchuckcanuck.com

Stainable wood fillers are one of those oxymorons. Will they accept stain? Yes, in most cases. Will it accept stain and look just like the wood it's in? In almost all cases, no. Even the homebrews such as sawdust and glue will not be exactly the same because the sawdust is bound to be mostly a mixture of long and short grain and the glue has served as a sealer.

I think you're better off to do the finishing and find two or three of the predominant colors and fill in with that. The wax sticks or putties made for this purpose work very well.

Here is a link that might be useful: installers putty

For paint-grade I usually use something like Elmers Wood Filler, which is water soluble.

For stain grade, I'll use a combination of already colored putties, similar to what my Uncle Bob linked to in his previous post.

Though I'm not a "fine woodworker" by any means, I've never seen a putty that simply took stain and then blended will with the adjacent wood. Near-invisible results can be had with putties and an artist's brush.

Mongo

Get a waterbased wood filler and mix in small amounts of acrylic craft paint until you get the color you want. This is what I do when finishing floors. I use Timbermate filler, but I mix it with Mixol tints until I get the color I'm after, but acrylic craft paint works fine too.