When I build new, I have used CertainTeed vinyl in the past (now known as PlyGem) probably the best builder grade vinyl with the best warranty response. I have also used Milguard and Atrium, both are just ok. Most of the times, were limited by the homeowners budget.
These days I like the Andersen 100 Fiberx the best, and usually spec these unless the homeowners budget doesn't allow for them since they are quite a bit more then traditional vinyl. I like the Andersen's because they are Andersen and it's instant brand recognition, they install well, and they seal well, so well when we do the blower door test the guys conducting the test can't believe how well the windows seal. Sure there are other fiberglass units and composites but we've had the best luck with the Andersen Fiberx line; it's the first line of windows where I haven't had a client ever call and ***** about problems with the windows.