We researched a few manufacturers, including Atrium, Milgard, Pella, Andersen, JELD-WEN, Penguin and Comfort Design Inc., and settled on the Comfort Series of CDI. Depending on your criteria you may end up with different manufacturers. Our criteria were relatively simple: vinyl, mid-grade, low-e, argon, competitive prices, good manufacturer and installation warranties. We needed a good window that won't break our bank, and whose u-rating is as good as the walls, and not more. The selection experience was not exactly a pleasant one - it felt like going through used car lots and talking to over-zealous salespeople who try to sell us their "good" used car. We found out though, that the installation company is as important, if not more, than the manufacturer. The same windows can be, and are being, quoted differently by different installation companies. Check manufacturer references, installation company references, and ask the manufacturer if they recommend a particular installer.
We had a great installation company who did it with the second best prices.