During the Bruma fight, the gates seem to just pop up, there didn't seem to be anything prepared on that place
Two possible explanations:
1 - simple game mechanic.
2 - the barriers between Oblivion and Mundus were further weakening and the creation of Gates is possible by this point without using Conjurers. You'll see a lot of gates appear at once in Imperial City during the final mission of the main quest as well.
thats interesting but that would take alot of Daedric Princes and alot of time. dozens of portals all opened at once so how could that be?
Other Daedric princes may have assisted Dagon. In a story written by former dev and freelance writer MK a couple years ago, Winged Twilights descend on a city in Morrowind. These are Azura's daedra. Who knows? It's unlikely though. She probably just lent some for Dagon's invasion. It might be well within his power to open dozens or hundreds of gates simultaneously. We're never given any real extent of a Daedric Prince's ability to focus his mind on hundreds of things at once. It's a cliche' god power so maybe Dagon can do it.
and what of the Great Gates? whats the significance of these "Great" gates?
Great Gates are apparently the big guns. In the Oblivion storyline they're apparently used to summon powerful Daedra such as Siege Walkers or Lord Dagon himself into Mundus.