I feel your pain. I too was in this situation a couple years ago. So I set out on a journey to visit where windows are made and talk to the engineers and people that build them. You have the obvious things to think about: Warranty, installer reputation, color, architectural fit, single hung, double hung, etc.
However, no one here is talking technically how to look at a window to tell if it is well made. So here it goes on what you should look for in a window. I will break this down into the following xx components: 1) glass 2) Fill 3) frame 4) lock 5) Counter Balance 6) energy efficiency factors.
1) The glass is typically made by two manufacturers in the US--Guardian Industries and PPG. The key technical factors are clarity in how well it lets in light, number of layers, coloration, type of glass and the coatings on the glass.
Depending on the climate you live in will determine how many layers of coatings and what side of the glass. The upper half of the US may want to have a coating on the inside of the outside pane and on the outside of the inside pane--this is so heat is reflected out in winter and reflected back in during the winter. Southern climates like Texas will just want the outside and may want two coats for extra reflectivity--especially on west windows. Coating technology is all about reflecting the heat and I have not had anyone convince me one is better than the other since I look for at the u-factor rating.
Today you can choose between double or triple pane windows. Triple typically gives you more insulating power. However, if it is a large window you open a lot it will be heavy. On large windows, 6'x6', you may not be able to get triple pane. Triple pane typically costs more. One advantage is the larger air gap between the windows.
Coloration is important because as a window that is coated allows light in, it can be tinted and cause the color to change in how you perceive it in your home. Some give more green to purple tints. I liked the Guardian glass and their coating process since it is more neutral and can enhance the colors in the room.
Clarity of glass is important and is called Visible Transmittance (VT). The more clarity the purer the glass and more likely more expensive. This may be important on a picture window but not on a bathroom window.
For those interested in sound insulation and security, look at having the outside pane be laminated glass--glass, plastic, glass. You can go crazy here in terms of bullet proof to enough to slow down someone with a baseball bat until the cops get there. For sound, look for a STC rating. Only if you live near a airport, crime ridden area or hurrican prone would I look to upgrade to this on a window because the costs go up multiple times.
Remember if you have windows near a door or drain, they have to be tempered glass. Check you local building codes for the distance. Doors are typically about 2 feet and drain about 5 feet. This can double the price of a window.
You can also choose sand blasted or acid etched windows of effect or privacy. More of a preference thing.
2) Fill. Most windows are filled with Argon and/or Krypton, but it is important how they fill it as well. Krypton is the better fill and at close to 100% as possible. Don't bother with a window not filled with either of these two gasses. The fill process is impossible for you to judge unless you see it produced. However, if the seller knows about their window it is important how they dry out and fill the gas in the window and then seal it. You typically have a spacer between the panes of glass. The best ones act as a descidant to abosorb moisture. Half inch is the min. space, but the higer end energy efficient windows are 1 to 1.5inches.
3) Frame. The frame materials can vary from vinyl, wood, fiberglass, aluminum and composites. Vinyl gives the best cost benefit but if you are coming from cheap builder grade aluminum windows just realize the vinyl frame is wider and means less light and glass to view though. The composites and fiberglass are nice but more up in price but give you more texture and color options. The key things to look for on a frame are how well are the seems welded together, and the seals around the frame. Look for a pocket for the window to go down into with three seals--one on each side to block air. For Vinyl, use of virgin vinyl is best and thickness is key--if you can bend the frame then it is not good--unless you are hercules. Look for multiple air channels in the frame so you have insulating pockets of air in the frame. For winter climates look for windows filled with insulation in the gaps. Southern climates do not need it--several studies on why this is true, those with PhDs in science can google them up.
Look for a metal bar in the vinyl across the center of the window where the lock is. This will provide more integrity and security to the lock on the window.
4)Lock. There are several out there. I like the ones that you can flick up with one finger and then when the window closes is auto latches shut. Remember the best lock is useless on a window since if someon wants in they just break the window.
5) Counterbalance. Your since and double pane windows have hidden in the side a spring that helps lift the weight of the window when opening and keeping it from slamming shut. I like the german made ones. The key here is quality if this is a window going up or down a lot. For bedrooms, this could mean life or death in the event of a fire. A good window will allow you to open and close it with your pinky finger with ease. Amazing that a 100lb window can move up and down with ease if balanced and installed right.
6) Energy Efficiency. Best for me to refer you to the agency that measure this for explanation.
Notice I did not mention price, but the reality is it is a factor for everyone but the wealthiest. You have to find the right balance for you among all the factors above. There are a lot of commission sales people selling bad products at high prices so beware. I ended up buying my windows from a local manufacturer, met the owner and he gve me a tour and explained why his product was better. Also, I was able to negotiate a better deal with him over his sales person because I was a serious buyer who took the time to see why he had a better product. So I got great triple pane windows for a price lower than the double pane at competitors and a perfect install job--installers knew I had a relationship with the owner who sent his best men to do the work.