There are specialty paints meant for this sort of craft. Get one that is made for glass, and choose according to the look you want (opaque or transparent).
The craft stores have paint expecially for glass. First use a template or draw on your design and then go over the design with the paint. Let the paint set for about 48 hours. It will not wash off.
Glas-tigues by DecoArt is a good brand of glass paint that you can either air dry or be heat set after a 7 day cure. Vitrail by Pébéo is another really good brand of heat set paint. It is very transparent so many layers of paint are needed for an opaque finish.
