Here's how to re-glaze those old, broken window panes. First, remove the old glazing compound with a propane torch and a putty knife. Carefully remove the old glass and clean the groove with a soft wire brush. Apply a thin piece of back glazing. Replace the glass and gently place push points every eight inches to hold the pane in. Apply a generous bead of fresh glazing compound and smooth it out with your putty knife.
For more on windows, consider:
Replacement Windows 101
How To: Replace Storm Windows
Fixing Old Double-Hung Windows (VIDEO)