There are many.
Found in the Cave of Origin as you go through the story.
The Regi trio have got the same legwork to activate. Before the three locations become available to you you must have a Relicanth and Wailord as well as a Pokemon with Dig and Dive. On Route 134 you must take the correct path through the currents to the patch of water you can Dive in. Once below folow the path up to the Braille inscription and resurface. Go to the next inscription and use Dig. Make Relicanth the 1st of your party and Wailord the 6th, then read that inscription. Three earthquakes will trigger and open passages on each respective route.
Regirock is found in the Desert Tomb, which is at the bottom of the desert in Route 111. Scribed on the walls inside is a message like the ones on Route 134: go right twice, down twice (best use the D-Pad for this) and then use Strength and the door to Regirock should appear. It's at Level 40, so be prepared.
Refer to Regirock for activation. He is located on Island Cave, a small island on the West part of Route 105. It requires Surf to gain access. Inside, there is a message telling you to wait. Wait in front of the door for two minutes and the door will open.
Refer to Regirock for activation. This one is located in Ancient Tomb in Route 120, west of Lilycove. Use Fly in the middle of the room and you will find Registeel.
Obtained through the Delta Episode.
Encountered through the Delta Episode. If you fail to catch it here, beat the Elite Four and head to the Sky Pillar to encounter it again.
You need the three other Regis for this. There is a girl in the north east house in Pacifidlog Town. Keep talking to her until she tells you a story of what her grandfather told you detailing things about Regigigas. Put all three of the Regis in your party, make sure Regice has a nickname and is holding a frozen item (such as Never Melt Ice or Snowball). Go to the Island Cove during the day and he will challenge you.
After fighting Groudon, you can go to Sea Mauville and look for the Scanner in the basement. You'll need Dive to get to there. Take it to Captain Stern in Slateport and he will give you the Clear Bell. Go back to Sea Mauville and on the deck there will be a portal. That's where Ho-oh is.
After fighting Groudon, go to the Scorched Slab. Go to the bottom of the cave and Heatran will be in the portal.
Mesprit, Azelf, Uxie
While soaring, if you have 3 Pokemon with max happiness in your party, there will be an island with a red star over it near Sootopolis called Nameless Cavern. Land there and in the portal will be one of the three depending on what time of day it is. You can come back to catch the others and different times of day.
Have Mesprit, Azelf and Uxie in your team and Soar. When you approach Dewford Town, you'll see a huge blue-green-black line. Approach and it will ask you if you want to enter. Say yes and you'll challenge Palkia.
Have both Palkia and Dialga in your party and the line will reappear. Fly into it and Giratina will challenge you.
Cobalion, Terrakion, Virizion
If you have three Pokemon with max EVs (you can see if the bar next to them in Super Training is filled up) and Soar, there will be an island with another red star over it near Pacifidlog. It's called Pathless Plain. There will be a portal there. It will let you challenge one of the three depending on what day of the week it is. You can come back to catch the others depending what day it is.
Have a level 100 Pokemon in your party and there will be a place near Mauville City that has a red star over it. It's called Fabled Cave. There will be a portal in it where Reshiram is.
Have both Reshiram and Zekrom on your party and an area called Gnarled Den, behind Mount Chimney, near Fallarbor, will open up with a red star over it. Kyurem will be in the portal. Use the Dowsing Rod to find the DNA Splicers in the cave as well.
Raikou, Entei, Suicune
Soar while having Lugia and Ho-oh in your party and a place called Trackless Forest near Rustboro will appear, having a red star over it. The portal will contain Raikou, if it's between xx:01 and xx:20, Entei, xx:21 and xx:40, and Suicune xx:41 and xx:00. You can come back to catch all of them.
If you have a Castform on your party and while Soaring, there will be a thunder cloud over Fortree. Tornadus is residing within.
Have both Tornadus and Thundurus in your party while Soaring and the thunder cloud will reappear. Landorus is within it this time.
Crescent Isle, where it is found, can appear randomly. It's a Mirage Island. It will appear south of EverGrande City, when it does.