How can I transition between rooms when refinishing hardwood floors?
I think that if you could make sure the stain/varnish colors match by refinishing both floors together, that would be your best bet. Unless the wood floors were installed at different times and have different grains/widths. In that case, no matter what you do the transition will be apparent.

If that that's the case, you might be able to do something decorative, with ornate wood squares or with tile, especially if you do it multiple areas of your house so that it echos the accent in more than one place. I know this is not the unobtrusive look you hoped for, but it could still look very pretty. If your kitchen uses small tiling, or if you have a fireplace with stone or tiling, or if you have any brick walls, you might be able to do a thin band of the same tiling/brick in the doorways, complemented by a border of the tiling/brick beneath your front door. See http://www.pinterest.com/pin/377739487469141226/  and  http://www.pinterest.com/pin/383368987001982461/.