Cool outdoor temperatures usually bring with them warmer ones inside as you turn on heaters, and this produces condensation that drips off the windows and wreaks havoc with the sashes that hold the glass in place. The finish goes first, and eventually the wood itself discolors and begins to deteriorate. Mold is one of the consequences, and that's a real danger for the toddlers in the house who like to sample whatever they can reach. You can kill mold and preserve the stained-wood appearance of the wood by refinishing. Oxalic acid bleach helps erase the black water stains.
Pry off the window stops with a pry bar so that you can remove the window. Once you've removed the stops, angle the bottom of the window toward you and pull it out. De-nail the stops -- you'll probably want to refinish them as well.
Lay the window on a flat surface with the exterior side facing up. Chip out the putty from around the window panes with a putty knife, then pull out the metal points with needle-nose pliers. Tap the glass gently with your fingers from the other side to loosen it, then lift it out.
Go over the entire sash with a wire brush, rubbing with the grain to remove as much loose finish as possible.
Mix a solution of 1/2 cup chlorine bleach to 1 gallon of warm water. Wearing rubber gloves and a mask, wash the entire sash with a sponge. The primary purpose of chlorine bleach is to kill mold, but it will also remove felt-tip marker or juice stains. Rinse with plenty of water.
Treat areas blackened by water contact with oxalic acid bleach. Dissolve enough oxalic acid crystals in water to make a saturated solution, which is one in which no more crystals will dissolve. Apply the bleach liberally to blackened wood with a sponge and let it soak in and dry. Apply it a second and third time if necessary. Neutralize the bleach with a solution containing 1 quart of water and 2 tablespoons of baking soda after you're done.
Sand the wood with 120-grit sandpaper, using an orbital sander for the places it can reach and sanding other areas by hand. Dust off the wood and sand again by hand, using 150-grit sandpaper.
Stain the wood with exterior stain, which will resist weathering and mold better than interior stain. Apply the stain with a paintbrush and wipe off the excess with a clean rag.
Apply two or three coats of clear polyurethane or varnish. Sand each coat lightly with 220-grit sandpaper when it dries and before you apply the next coat.
Replace the glass, pushing in new points with needle-nose pliers and applying fresh glazier's putty with a putty knife. Set the window back in the frame and replace the stops.