Are the rotting windows and window sill salvageable?
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.