I want to make a mortise and tenon joint that will be held together with a dowel instead of glue. How can I drill the hole in the mortised stock and the tenon so that they line up accurately and produce a tight joint?
The simplest solution is to drill the dowel hole after you fit the joint together.
Fit the joint and make sure everything's square and true, then drill straight through the mortice and tenon in one go and insert the dowel. Chisel/plane and sand it flush and you should be good to go.
Making a mark on the outside of the mortice where you want to drill will ensure you get the location right.
ChrisF's solution will provide you with nice, stable drilling support and it will make sure the holes line up perfectly on both parts. But if you don't want to use glue, keep in mind that it's not necessarily a bad thing if the holes don't line up perfectly; in fact, there is a specific technique called "drawboring" that requires this and makes an extra-strong joint.
Basically you drill the hole slightly off-center in the tenon and then chamfer the inside end of your dowel. This makes the mortise pull the tenon in mechanically as you pound in the dowel. The technique is the subject of a recent Wood Whisperer video: http://www.thewoodwhisperer.com/videos/drawbored-mortise-tenon/