After getting the National Dex, you can get the following Pokemon:
Magnezone (#462) Catch or import a Magenemite, then get it to Magneton at level 30. Go to Mt. Coronet. Level your Magneton, and it will evolve. Rhyperior (#464) Get a Rhydon by leveling a Rhyhorn (Route 227 and Stark Mountain) or catch Rhydon (Routes 227, 228, and Stark Mountain). Then, trade it while it holds the item Protector. It will evolve into Rhyperior.
Magmortar (#467) Import Magby or Magmar, or catch Magby on Route 227 or Stark Mountain with Pokemon Leaf Green in your DS. Trade Magmar while holding Magmarizer to get Magmortar.
Togekiss (#468) Import Togepi or Togetic, or catch Togepi on the small island on Route 230 using Pokeradar. It is rare but easily caught with Max Repels. Use a Shiny Stone on your Togetic to get Togekiss.
Rotom (#479) Go to Eterna Forest, and enter the Old Chateau. Find the television that is flashing, and interact with it until it asks you if you want to thwump the television. Do so, and Rotom will apear. There is only one, and it is level 15. Either bring low levels or very high ones, and just use Ultra Balls.
Heatran (#485) After getting the National Dex and defeating the Elite Four, go to Stark Mountain. Go inside the mountain, and travel with Buck. Go to the end of the mountain, and he will take the Magma Stone. Exit the cave, and fly to the Staging Area. Go inside one of the normal houses, and talk to Buck. He will return the stone. Go back to Stark Mountain, and go to where Buck took the Magma Stone. Heatran will be there. It is level 70 and is a Fire-Steel type. Its final move is at level 96.
Regigigas (#486) Import all three Regis from Pokemon Ruby, Sapphire, or Emerald. Have all three in your party, and fly to Snowpoint City. Go into the temple there, and make it to the basement. Regigigas will be waiting there at level 70. It is a Normal-type and very strong, but has one major drawback. Its Slow Start ability cuts its Attack and Speed in half for five turns after each time it is switched into battle. Its final attack is at level 100. For Isgiga Impact, just buy the TM if desired. Go to the Move Tutor, and Regigigas can learn all the punches. Giratina (#487) After getting the National Dex and defeating the Elite Four, go to the Spring Path off Route 214 that opened up. Go into the cave, and find your way to Giratina. It is a level 70 Ghost-Dragon type with powerful stats and moves. It learns Lucario's Aura Sphere for its final move at level 90.
Cresselia (#488) Go to Canalave City, then go into Sailor Eldritch's house. There will be a boy in a bed and a woman. Talk to both of them, and Sailor Eldritch will ask if you want to sail to Full Moon Island. Do so, then go deep into the island and look at Cresselia. It runs off, and you must use the Marking Map Poketch to find and capture it as if it were Mesprit. It is a level 50 Psychic type and has surprisingly good stats all around for a level 50. It learns three signature moves at levels 66, 75, and 84. Its final move is Psychic at level 99. Phione (#489) Hatch an egg transferred from Pokemon Ranger. Raise Manaphy, then breed it to get Phione. Phione does not evolve into Manaphy. It is a moderate Pokemon in terms of stats. Rain Dance is its final move at level 69. It learns many typical Water-type moves, being a Water-type.
Darkrai (#491) Darkrai is only obtained through a hack or a special item from a licensed Nintendo event. Use the item, then sleep in some hotel. You will wake up on an island, and you then can try to catch Darkrai. This Pokemon is extremely powerful. Its ability causes one eighth health damage every turn to sleeping enemies. Its final move is at level 93, Dark Pulse; but its best move is Dark Void. It puts both enemy Pokemon to sleep with 90% accuracy.
Shaymin (#492) Shaymin is only obtained through a hack or a special item from a licensed Nintendo event. Use the item to go to Flower Paradise to find Shaymin. You must capture it there. Shaymin has average stats but is a strong support Pokemon for duo battles. Its final move is Seed Flare at level 100. This is a moderately good Grass-type Pokemon.
Arceus (#493) Arceus is only obtained through a hack or a special item from a licensed Nintendo event. If you get this item, go to Spear Pillar's Hall Of Origin, and use it. It will produce a staircase. Save the game before you reach the top. Once you reach the top, you must battle. This is one of the highest level legendaries since Pikachu in Pokemon Red. It is either level 80 or 90. It has very good stats and is a Normal-type. Its ability allows it to change type, based on what Plate it is holding. For example, if it holds Dragon Plate, it is a Dragon-type. Its final skill is at 100, Judgment. Judgment's type is based on what plate you have equipped. It does 100 with 100 ACC and 10 PP.