really depend on the design of the book shelf/shelfs i myself would problaly use a rebated joint as they are quick to make i=with both hand and powere tools, if you don't want to see the joint you could make it a half houseing ( quite difficult if not got a router) or a dowl joint/ biscit joint ( both need jigs/spesilist tools) or cut some very small mortis an tennons (about the with of the shelf square)
if you were to tell me more about the design you are using i would be able to advise you further
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