well as i mentioned up-thread, i'd not go so far as to say i never encounter the popup - and, frankly, it doesn't bother me when i do.
though, at least with military units, i have certain cities which produce my military units - and i queue up, say, 10 cavalry or 10 artillery or whatever at a time - and if i do need to modify it, i am reminded that i can do that buy having to do my promotions of these units once they've been completed.
i usually only queue crucial buildings in groups of 2 - 4.. you know, say, with a new city queue a granary and then a theater, adding on a lighthouse and a harbor if it's a sea city... that kind of thing - or i'll group together a couple of religious buildings in a queue - two temples and a monastary, for example... also, with markets banks and grocers - i might queue those one right after the other.
so, i guess, in fairness i do both. i had previously been thinking about military units, which i never want to scroll and select every 2-6 turns or whatever... i definitely mass queue them.