I opted to use a "cross dowel" to allow for a strong connection that can be easily and quickly assembled and dis-assembled. A cross dowel is a small metal rod, with a 1/4-20 threaded hole through it and a slot cut across the top to aid in alignment. I got mine on sale at Rockler woodworking (www.rockler.com).
Since many of the assemblies were too large to fit in my small benchtop drill press, I made a quick-and-dirty drilling jig that worked perfectly. I used brass inserts (1/4" and 3/8") to protect the wooden jig from repeated drilling. I clamped the pieces together, with the drilling jig and - perfectly aligned holes, every time.
Here's how the finished product came out. They are nice and flush with the wood surface, hold the thing together beautifully and are easy to un-do and re-do quickly and neatly.