The windows I chose are high-efficiency vinyl replacement windows. I could only find one manufacturer that made a dark brown vinyl efficient window (U-factor .32 and SHG .29 with the Low-E and Argon package). The brand is Softlite and I purchased them from Norandex/Reynolds in Nashville, TN. They're very reasonably priced (much less expensive than Anderson or Pella clad windows), and they are actually more efficient without spending a fortune.
This picture and the next couple of pictures show how the window looks before trim-out, so you can see how it integrates with the logs to allow for shrinkage. Really very simple.