My windows and window sill have rotted on the bottom. The quote for the windows without installation are thousands of dollars. Could this be salvaged with epoxy, bondo, and making frames for the glass? The top portion is solid.
The frames for the glass are the least of your worries as they are removable.
You could attempt some sort of patchup job with bondo and paint, but it wouldn't remove the problems that caused the rot and it would be very difficult to actually bond to partially rotted wood. Your goal would be to cut out all the rotted wood, reinforce the structure if necessary, fit wood to replace as much as possible and then re sculpt the frame with the filler product. The difficulty level of getting decent fit and finish is incredibly high, let alone the difficulty of accomplishing a good seal and shape at the same time. When it leaks or the edges start to rot out again, you're back to square one with the addition of a potentially extremely difficult and complicated to remove section.
You could attempt to properly repair the frame, but that might involve anything up to completely uninstalling the window, replacing any flawed pieces and reinstalling it. This would normally only be done to protect or restore pieces of historical or sentimental value. You could get a quote on it, but it's likely to exceed the cost of new windows. You try not to throw away burled walnut or bubinga, but for common wood, the labor is worth more.
If you don't already know how to do this and want to do it yourself, the carpentry skill and tools could also exceed the cost of the new windows. That said, it's not impossible, just a lot of skilled work. You can do almost anything with fairly basic tools and ample expertise, but the right tool can turn a 9 hour task involving great precision into something you can do casually in under a minute.
Lots of good information above. Here's a slightly different view on the matter. (Professional carpenter here; have built traditional windows/doors.)
First, you've gotten a quote that seems high for replacement. That might be the real price for the quality of product you want, or you might have found the most expensive distributor in the town. Get a couple more quotes, and if money is an issue, talk to them about less expensive (typically less attractive/ less durable) windows. Also, you have a structural corner that I expect will turn out to be at least soft and possibly rotten that you need a modest contingency budget for. At the end of the day, "thousands of dollars" might be tough to swallow, but it represents a tiny proportion of the value of the house. If you had to, you could cover everything with plywood, slap a coat of paint on the outside, insulate and plastic inside and wait a few years.
With regard to the window itself, this is a complete rebuild. I'll say that again: there is nothing left of these windows. (You don't even want to try to rehab the glass, as it'll fail soon enough and you'll be cursing your choices.) If you consider your cost of your time to be zero, you're still investing lots in tools. (Norm Abrams or Roy Underhill could build this with cheap hand tools, but I can't.) Don't get me wrong -- tools are great, but you have to make a conscious decision to divert thousands of dollars and countless hours to this project. And if you end up getting these built by a pro, you're way above the cost of a factory product for no good reason.