Wash the windows with a mild cleanser and water. Scrub persistent debris, stains or other materials stuck to the windows. It's best not to pressure-wash windows as this can cause additional problems including glass breakage. Use a scrubber, scraper and one-sided razor blade to remove old caulking, glazing and paint.
Spray and scrub moldy areas with 1 part bleach to 3 parts water in a spritzer bottle. Spray the mixture directly onto the mold and allow the mold to turn white. This means the mixture has killed the mold, which can take from 15 to 30 minutes. Clean the area as you would normally after the mold is killed.
Scrape along wood joints and seams with a putty knife and 5-in-1 knife. Sometimes putty and caulk fail without visible signs until you drag your putty knife along the area and the materials fall away. Use the tip of the knife to dig out difficult caulk. All of the caulk should be replaced during the window painting process. Sand the window with a palm sander, sanding block and 100-grit sandpaper.
Repair small windowsill cracks with elastometric sealant. Repair larger cracks by cleaning the crack, priming the crack with an oil based primer and allowing the crack to dry for 24 hours. Fill the crack with auto-body filler (bondo) or wood filler. You may need to apply several layers of wood filler to bring the surface up to level. Allow the filler agents to dry and then sand the sill.
Fix small areas of rotten wood by digging out the bad wood with knives, scrapers and other tools. Soak the remaining wood with a wood hardener. These are often epoxy-based. Follow the manufacturer's directions for best results. After the wood hardener is dry, apply your auto-body filler and wood fill to build up the area so that you can sand and finish it properly.
Prime all exposed and repaired wood surfaces with an oil-based primer and allow the primer to dry for 24 hours. Fill all cracks and seams except the functioning parts of the window with elastometric caulk and a caulk gun. Be careful to leave weep holes and the sash uncaulked so they can operate properly.
Glaze all areas of the glass where you have removed old glazing or where glazing is missing. Glaze over primed wood. Warm your can of glazing in warm water for 30 minutes and then set your glazing can in the sun to keep it warm. Gather a ball of glazing and work the glaze until it is warm in your hands. Roll a rope and press the rope between the glass and the wood firmly. Drag a putty knife or glazing knife through the glazing at a 45-degree angle. Remove excess putty as you work and smooth the finish with your fingers. Allow the glazing to dry for 24 hours before final painting. Prime with an oil-based primer any areas of your window that remain unprimed.
Open both sashes on a double hung window to an overlapping condition before painting. Paint the entire outer sash and as much of the inner sash as you can reach. Reverse the sash positions to paint the unpainted portions of the inner sash. After the paint dries, raise both sashes and finish painting the jamb. You can use either an oil- or acrylic-based paint.
Paint casement style (crank-out) windows edges first. Paint the top, bottom and sides and allow them to dry completely. Apply paint to the top and bottom of the sash, the sides and then the frame. Paint primers and paints onto the glass and clean the glass later with a one-sided razor blade. This will create a seal between the wood and glass. Add an elastometric clear caulk to seal the joints further once the paint has dried completely.