Help decide course of action for rotting windows
If your timeframe is inside 5 years, you probably can't make an economic argument for new windows. 

Suggest you attack one (neither the worst nor the best) and see what is in there when you pick away at it. New storms are easy. Brick mould is easy. The sill might be a little harder, but patience is a virtue.

Depending on the level of rot, don't immediately rule out bondo and/or capping the sill in aluminum. 

If you don't have one already, get an oscillating tool. It'll pay for itself in this kind of work. Battery powered is vastly better than corded in my opinion.