I ordered my windows right after I thought I had my final floor plans. Nonetheless, I took Jay Shafer's recommendation made in the Walden Plans -- the original set of Tumbleweed plans I purchased. I bought seven Jen-Weld, Low-E, Tempered Glass, ENERGY STAR®, Awning windows. I ordered clear lacquered wood inside and white aluminum clad on the exterior. [http://www.jeld-wen.com/catalog/windows/awning] Unlike the Walden, I chose different size windows: 32hx34w for the living/dining area, 20x30 in the kitchen, 20x24 in the bath and gable end loft (20x24 is a legal egress window allowing escape from the loft and bathroom should there be a fire in the kitchen.) I also bought the tiniest window Jen-Weld offers for the gable end above my box window. They are indeed beautiful, well made....and very expensive...roughly somewhere around $500/window. I had a 10% off coupon at Lowes which helped but my wallet is still in pain.
I did make one error. I ordered non-clear/opaque glass in the egress windows. I can live with the opaque glass in the bathroom, but I reordered the window for the loft. I was fortunate to have had a good relationship with the guy in mill works (he suggested the opaque glass in the bath) so he allowed me to return it and reorder it. Apparently, you cannot replace the glass and retain the warranty. Anyway, neither of us discovered the error until I brought the windows home. This could have been a costly mistake. Thank you, Lowes!
Take your time when ordering and ask at the pro desk who is the best person in Mill Works. Not everyone in Mill Works knows are experienced in ordering windows. There are so many options to consider, you need someone who can explain the choices and not rush you while you are deciding. The order form specifies the rough opening (RO), so you could frame your walls with those specifications without worry. They will not be installed until after the roof is installed.