There are literally tons of manufacturers of windows. Lots of "ma and pa" shops that make, build, and furnish windows. The bulk of my business in the past has been selling plastic to window manufacturers.
With the smaller shops they will often come fit the window to the opening available (if you live in Texas, they brick around the window surround, making it a bitch to install a new window) and will build the window to whatever specs you want.
The best quality windows I've ever seen were from a small shop I sell to out in the middle of nowhere. For what you pay from the box stores, you can buy a nice set of windows from a shop that ONLY builds and installs windows, get professional installation assistance and someone that will more than likely stand behind their products.
I have known some looney businessmen/women, but they are found in all sectors. Check out the internet for people who may have bought windows from the smaller shops, or ask for references and contacts of people who have their windows.
Be sure to do your research on what you want and what is available. Remember, an informed consumer is a good consumer.