If a small area of a wooden sill is rotten, but the rest of the window is sound, you can just replace this part of the sill.

Cut back the sill to sound wood. Use it as a template for the patch. Mark the position of the groove under the sill (the drip groove).

Cut the patch slightly larger than the rotten section you removed. Use a router to cut out the drip groove. Screw the patch in place and then plane it smooth. Make sure to countersink the screws so they won’t be in the way of the plane.

Other wooden frame repairs
Another option for fixing loose joints is to strengthen them with dowel.
If a whole section of your window is rotten, then pry the piece out and make a replacement, using the old section as a template. If rot is more widespread, you should replace the entire window.