Dragonite: Super Rod in the Syxten Bit cave, room before THE fight, where Sneasler and stuff hangs out.
Salamence: After you fight Talon on top of GDC building you can talk to him again in his home and he will ask you to explore the rest of the Tyluric temple. Do that (you need Rokidee, Gligar/Gliscor and Emolga/Kilowattrel), trade him a Togepi (don't forget to breed it beforehand).
Metagross: Helojask island, drop i believe 15000 essense into the Den there once you can use Strenght.
Garchomp: Sitting in the Zone zero, explore it again, find a key, open apartments, press a lever, very straightforward.
Hydreigon: End of the Ana's questline.
Goodra: End of the Goomink questline.
Kommo-o: Do a short sidequest near Badlands entrance for an Aevian Jangmo-o (very right of the desert), it appears very late so just check it after late badges. After that trade one in the desert house nearby for normal variant (don't forget to breed).
Tyranitar: Atebit world, around Allen and Alice's house after you come back there by yourself.
Dragapult: Nope.
Baxcalibur: Nope.