Cobalion - Route 13
Cobalion will jump out, and then stand in the middle of the route, welcoming you to your doom, as the Pokedex description writes, "It worked with its allies to punish people when they hurt Pokémon". With Cobalion out for vengeance, you are forced to catch it or... kill it with your prized slave Pokemon. Ha! You encounter it once before, but do not get to catch it until you reach this area the first time. It awaits at Lv. 45, unless you've defeated it the first time; in which case, it will await you at Lv. 65 - having stolen a bunch of Rare Candies, as it cannot defeat other Pokemon for experience, in the same spot after you defeat the Elite Four to regenerate it.
Virizion - Route 11
Virizion, like Cobalion, suddenly appears while you're walking along the route, much like a Creeper, being green as well. It stands in the center of the route after jumping out, even while the place is frozen, clearly showing its intention to assault you while you are stunned by surprise, much like its Pokedex description, "Legends say this Pokémon confounded opponents with its swift movements.". Just like Cobalion, it is at Lv. 45, but will be Lv. 65 if you defeat it, then the Elite Four, and return.
Terrakion - Route 22
Terrakion, unlike the other two, does not pop up. It's already standing there because it's not a little scaredy-cat and faces challenges like a man. Before you can get near it, Colress will speak to you and then give you his pointless machine that removes the Crustle down south. After that, you can interact with Terrakion in more ways than one. Like its fellow musketeers, it's at Lv. 45, and becomes Lv. 65 when you defeat it and return after defeating the Elite Four.
Zekrom/Reshiram - Dragonspiral Tower
These two require a sidequest to be done, in which you battle N, who uses only the dragon he had in the previous game because he's afraid of change. Upon defeating him, the dragon returns to its stone form and N gives it to you, seeing that you are indeed, the truly greater trainer and the supreme leader and commander of all Pokemon. Take it to Dragonspiral Tower, and the dragon will revive itself and await you to challenge it, despite it knowing the consequences - getting trapped in tiny balls for the rest of its life. They are both Lv. 70, having just come out of 69.
Kyurem - Giant Chasm
Kyurem will be in its old habitat because it can't afford to pay the movers, or rather, because no movers want to help it move, seeing their comrades being eaten. Since you cannot catch it the first time and are forced to beat it down, you have to return here. You must also capture the Zekrom or Reshiram to be able to encounter Kyurem, because Kyurem's shy and won't let itself get close to other people without a friend. Once you capture it, it leaves behind the DNA Link Pin, which fuses the dragons together in a strange bonding experience. Kyurem is set at Lv. 70, much like its friends.
Latios/Latias - Dreamyard
The Lati twins are back for mischief, and will play a little "game" with you in the Dreamyard before allowing you the chance to capture them. When you finally catch Latios (B2) or Latias (W2), Soul Dew will be left behind. Both are Lv. 68.
Uxie - Nacrene Museum
After first encountering them with Professor Juniper in Heart Cave, the Pixie trio will scatter around the region. Uxie awaits you at Nacrene's Museum at Lv. 65. You must step on a certain tile outside for it to appear.
Mesprit - Celestial Tower
Mesprit has fled to the top of Celestial Tower. It requires you to step on a certain spot just like Uxie, and will be available at Lv. 65.
Azelf - Route 23
Azelf sits in a corner off to the left side of Route 23. Yet again, it will be Lv. 65 and you must step on a certain tile.
Regirock/Registeel/Regice - Underground Ruins
Unlike previous games, you can catch all three Regis in one area. The difference is that you can only obtain Regirock at first, and you have to solve a puzzle which can only be discovered by visiting the area at day then at night. After obtaining Regirock, you will unlock the Steel Key in Black 2, and the Iceberg Key in White 2. You must activate the key via the Unova Link, and then you can obtain the respective Pokemon. You can obtain all 3 in one game if your friend shares the other key with you via Unova Link. All 3 are Lv. 65, further confirming that there is some villainous work going on keeping all these trio Pokemon at level 65.
Regigigas - Twist Mountain
Regigigas awaits you and the other three Regis within Twist Mountain's depths. The statue will not move because it just can't get it going unless you have gathered all 3 Regis in your "party". It will be at Lv. 68, dominating the other 3 Regis.
Cresselia - Marvelous Bridge
After you grab the Lunar Wing from the Abandoned House near Lentimas Town, you can take it to Marvelous Bridge and Cresselia will appear when you reach the center, seeking to recover its ugly pink wing. It is at Lv. 68, which appears to be a trend here...
Heatran - Reverse Mountain
To encounter Heatran, you first have to find the Magma Stone on Route 18. When you take it to a deep cavern inside Reverse Mountain, Heatran will drop down from above, missing its intended target - you. It will be at Lv. 68 as it attempts to assault and eat you.