How do I reglaze my garage door windows?
Most likely you want to use window glaze more then caulking.  eHow has an 'ok' article on the differences, but is lacking some better detail.  However, there was a similar question on yesterdays contractor.com and the answer from Billy NY is excellent.  He covers the main reason to use glazing over caulking in certain situations, primarily when mixing substrates such as glass and wood.  He also mentions that silicon caulking can work well in some instances, but can't be painted where as window glaze can.

If you do re-glaze your window, popular mechanics has a great 'how-to' article with step by step directions.