As I progress (slowly) on the design of the pergola I'm putting in my
back yard, and as I get to the point where I'm stacking the
criss-crossing rafters together, the thought crossed my mind that
instead of toe-nailing them together or driving screws down at an angle
(or using those ugly galvanized metal brackets), couldn't I drill 3/4"
holes and use dowels and glue to fasten them together? Dumb idea? If
not, what kind of glue would you use? Titebond III? I'm using
untreated Western Red Cedar, BTW.

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See Nad. See Nad go. Go Nad!
To reply, eat the taco.