I have put Milguard in many homes.

I have been very happy and so have the next owners. - If one fogs - call a number give them the s/n on the window and someone comes out and replaces it.
Never heard of them, but that means nothing. There are thousands of regional companies that do great jobs.
In the end the installer is key. A great installation of crappy windows will typically be better than the best windows installed like crap.
Windows are typically the #1 source of heat loss or gain in a house so devoting your time to insure it's done right with superior products will save you money as the homeowner and will help sell the house if the windows are top notch and installed correctly. Obviously if your in a blue collar hood like i am - don't overdue it and make the nicest house on a crappy block if you plan on moving anytime soon.
Some general factors I would consider to be important:
*Company lifespan. If the company hasn't been around more than 20 years - avoid them. Lifetime warranty on a company that claims chapter 11 and changes names every 5 years isn't going to help you in ten years when all their windows fail.
*Installers work full time for the window company. Do not use installers subcontracted by the window company.
*If the window company can't tell exactly which Low-E glass is in the window and will not get you the information - run away. That means they are NOT producing the insulated units themselves and are basically clueless. This can cause major issues when it's warranty time.
*Glass thickness is key. Get the thickest glass you can. Cheap windows will have cut corners here.
*Warranty. it had better be lifetime to the buyer and even better if transferable to another buyer.
*Only buy windows with tempered glass. I don't care if code allows them to be annealed - buy tempered. It's 4-5 times stronger and could save someones life. Skimping a dollar or two per sqft is not worth having weak/dangerous windows.
*If you have UV/noise/burglar issues - look at getting the inboard lite of glass laminated. While it's not as strong as tempered it's great for blocking noise and slowing down smash/grab intruders. For example your windshield is laminated - your side windows tempered. Lami also blocks 99% of UV rays thus stopping fading in your house. Outboard lite to still be Low-E.
*Vinyl sucks. I love wood clad windows, but I'm old-school. They expand/contract much less and are typically better quality IMHO.
I have been getting all my Anderson windows from Home Depot. They are builder grade so while Anderson is good - these are the cheap ones. Some are ten years old and the great thing is I can still to this day buy the same exact window. Thats good for me because I still need to replace a few more. Also good if your on a budget and can only afford to swap out some at a time.