Your windows are the most likely culprit for heat loss in your home. This is especially so if the windows are older and not sealed as well as they used to be. Fortunately, you can spend a little bit of time and work to make sure that they are in as good shape as possible.
First, you want to check that there are no cracks around the window. These can let a lot of air escape and should be sealed well. You can use a flashlight and shine it around the edge with someone spotting on the other side to find any cracks. If you find cracks, use weatherstripping and caulk to seal them up.
If you find rot in the wood around your window, it is important that you take the time to clean it up very well. Just a little bit of rot left behind will continue to eat away at your window frame. It is better to cut away some of the healthy wood to make sure nothing is left.