Some legendaries are weird with their conditions, like walrus said, I think some might be time specific like the lake trio seem to be. Others just have certain conditions that have to be met. I heard that you have to have both Lugia and Ho-oh in your party to find the dogs, but I found them with only Lugia in my party (which you can catch at Sea Mauville by the way, and it's Ho-oh if you have Omega Ruby).
Cresselia is up to pure luck as far as I know, you have to just wait until you get Crescent Isle from SpotPass or whatever.
To catch Thundurus(AS)/Tornadus(OR) you have to have Castform in your party. And of course to get Landorus you need both in your party.
For Zekrom(AS)/Reshiram(OR) I have no idea, I've heard that you need a level 100 in your party but not sure, and for Kyurem you need Zekrom and Reshiram in your party.
Dialga(AS)/Palkia(OR) require the lake trio in your party, and Giratina requires both Dialga and Palkia, as expected.
Regigigas is a bit complicated. You need all 3 Regis in your party and your Regice needs to be nicknamed. It also needs to be holding either a Nevermelt Ice, Snowball or Castelia Cone, I've seen people say that any of these work but I've also heard that Nevermelt Ice is the most reliable. Regigigas will be in the Island Cave north of Dewford where you found Regice. He doesn't have an ingame overworld model (inb4 lazy gamefreak) but if you go to the center of the back room the battle will initiate after a text box. Lastly, there is some weird shit regarding time with this one. Supposedly the most likely time to encounter him is between 8 AM and 6 PM. If he isn't there just check back every 30 minutes or so.
Oh and Heatran is in the lowest level of the Scorched Slab on route 120