Bryan pretty much summed up what I was trying to explain to him the other night. It's basically a slow, steady procedure where water and electricity come hand in hand....yum! Glass is very tricky to work with and can be very difficult to drill through. The best method that I have found, is like Bry said, to use a drill press and lightweight drill. I have found some pretty inexpensive mini (tabletop) drillpresses at Sears as well as some small project Black and Decker drills. Search around for the best price...especially if this is a one time project. You will need a diamond tipped drum bit for this and the size is dependant on the size of hole you want to cut. I purchased mine on e-Bay for 15.00 but some can get pretty expensive. Once you have decided on where you want the hole to be drilled, take a permanent marker and draw a hole around the bit, onto the glass. Next obtain a nice size chunk of moldeling clay (enough to make a 4" high ring around the hole). This ring should extend a couple of inches from the initial hole and filled with 1 to 2" of cold water and an ice cube or 2. The key here is keeping the drill bit cool and lubrocated so that the drilling is smoother and less 'violent' on the glass. Also, it is very important to check and make sure that the glass you are drilling is NOT tempered glass as this cannot be drilled through. Once you have the hole and clay ring 'pool' prepared, lay the drill press directly on the glass with the drill and diamond bit attached. Position the bit directly on the hole you drew. Set the drill press so that the drill's weight will pull it down. The weight of the drill is sufficient in keeping pressure on the bit and glass so that it is cut at the right pace...too much pressure could result in a disaster. Turn the drill on and keep your hand right under the drill press arm so that when the drill bit penetrates the glass completely, it does not slam down onto the glass and break it. You should now have a nice size hole and a little glass disc to show for it.

Email me or post here what you intend to do with this hole and if I can be of further assists, I'll help you out the best I can. Good luck and feel free to contact me!
-Bill J.