Remove as much of the old window as possible.
Keep in mind that old wood framed windows usually have several small metal triangles that hold the glass to the inside wood frame. Use care not to loose these as you will use them to replace the broken window.
Remove as much of the old window putty or calk as you can witout gouging the wood too severely.
Measure the frame for the size glass you will need to effect the repair.
Go to your local glass shop with the window measurements and order the correct size window glass for your repairs. You may want to order extras to replace any other worn or broken windows later.
Push your new window into place using care to use an even pressure and not to force window glass as it can break.
press the metal window triangles into place using care to try to put them into the same holes you took them out of, if at all possible.
Apply small amounts of window putty all along the window frame and press into place.
Follow with more window putty if needed and smooth to create a nice angled seam between the window frame and window glass and making sure that you cover up the metal window triangles
Allow 24-48 hours before you repaint the window frames to allow the portion of the putty that is exposed to the air to harden.