I just did a project using Minwax Natural stain #209. It was suggested by one website that using the Natural stain as a first coat would help saturate the wood, so that when I put a darker stain on as a second coat, it would not penetrate so much and have so many blotches. As per that suggestion, I don't know if it really worked that well, and if I were to do it again, I'd just buy the pre-stain conditioner instead.
But as for the effect of the natural stain... I applied it to white pine. After staining with the Minwax Natural, the appearance of the wood was very similar to what it would look like if the pine was just wet with water. Grain and knots look a bit darker and clear areas have just very VERY slight hint of a yellowish cast. I skipped the stain and just put polyurethane on the shelf boards for this project - they look exactly like the piece that I applied the natural stain on.