Section 1: Breeding Preparations 1

The Magma Armor/Flame Body effect(DP)
A Good breeding feature introduced in Emerald is an additional effect that Pokémon with the ability Magma Armor or Flame Body have during the game.
Eggs need warmth, right? Having a Pokémon with this ability in your team will reduce the number of steps you need to Run/Ride for the egg to hatch by roughly half. The word ‘roughly’ here will be clarified later on in Section Three of this part of the breeding guide. Here is a list of Pokémon that can have Magma Armor and Flame Body: Magma Armor: slugma, magcargo, camerupt
Flame body: magby, mamgar, slugma, magcargo
Make sure you've always got one of these in your team while breeding in D/P.
Because Slugma and Magcargo both only have Magma Armor or Flame Body, we're going to work on capturing them. They can be captured from various games. Remember, their out of battle effects work only in DP, so if you get a Slugma from outside DP, you need to transfer it to Emerald, Diamond or Pearl for Magma Armor or Flame Body to have their step-to-hatch reducing effects.
Ruby, Sapphire and Emerald: Slugma is found 10% of the time on the Fiery Path. In addition, in E, Slugma can also be found in Route 113.
FireRed and LeafGreen: Slugma will always appear on the third basement floor of Mount Ember. If you use Rock Smash on the same floor, Magcargo appear 10% of the time.
Diamond and Pearl: Start by heading north from the Resort Area, onto Stark Mountain. Go inside Stark Mountain itself, and walk around the first area. You've got a 35% chance of getting either Slugma or Magcargo; capture it when you see one.
Other: In Colosseum, Roller Boy Lon of Pyrite Town has a Slugma, and in XD: Gale of Darkness, Cipher Peon Kolest in Citadark Isle has a Magcargo.
The Everstone Hold Item (EDP)
In EDP, if a female Pokémon is holding the item Everstone and breeds with a male Pokémon, the baby will have a 50% chance of having the same nature as the female Pokémon. This also works if the Pokémon holding Everstone is Ditto.
To be perfectly clear, these are the four different ways to transfer a nature 50% of the time to the baby:
* A Male Pokémon breeding with a Female Pokémon holding an Everstone results in the baby having a 50% chance of having the same nature as the Female Pokémon.
* A Male Pokémon breeding with a Ditto holding an Everstone results in the baby having a 50% chance of having the same nature as Ditto.
* A Female Pokémon breeding with a Ditto holding an Everstone results in the baby having a 50% chance of having the same nature as Ditto. (Even if both the female Pokémon and Ditto hold Everstone, it will still be a 50% chance of the nature being transferred, and it will always be the Ditto nature that is transferred to the baby. Also, Everstone will not work if it is being held by the female Pokémon while being bred with Ditto.)
* A Genderless Pokémon breeding with a Ditto holding an Everstone results in the baby having a 50% chance of having the same nature as Ditto.
If you breed in DP, it is possible that Everstone won't work. This happens if you breed two Pokémon that originate from different language versions, for example an English Emerald Ditto with a Japanese Diamond Chimchar.
Everstone can also be found in various games. Remember that Everstone’s effect in breeding works only in EDP, so be sure to transfer it to Emerald, Diamond or Pearl if you find one outside of these three games.
Ruby, Sapphire and Emerald: An Everstone can be found in Granite Cave.
FireRed and LeafGreen:You can get an Everstone in the Pokémon Center near the Rock Tunnel.
Diamond and Pearl: Everstones are extremely common in the Sinnoh Underground. Just keep mining.
Ditto: Breeding Champ
As should be clear from the previous section, Ditto's a valuable Pokémon to have, since it can breed with every breedable Pokémon, and it can also transfer its nature 50% of the time even to genderless Pokémon like Staryu, if it is equipped with the Everstone item. You might be saying, after reading all this: "Okay, let’s see if I’m understanding this correctly. I need a Ditto with a Timid Nature and a 31 IV in Speed in order to breed it with my Gastly, so that I can get a Timid Gastly with 31 Speed IV, right? But from where am I going to get such a Ditto?” The short answer is: you need to catch it. I can hear groans of disappointment, but cheer up: this is actually not very difficult to do.
When a wild Pokémon is encountered, the IVs for that Pokémon are generated completely at random. This means that there is a 17.3% chance (about 1 in 6) that a Pokémon caught in the wild has at least one of its IV to be a perfect 31. All we need to do, then, is to catch six Ditto, each of which has a perfect IV in one of the six stats.
However, we also need to ensure that its nature is the one we’re looking for. This can be done using a Pokémon that has the Synchronize trait (only in EDP). In EDP, if the first Pokémon in your party has the Synchronize ability (trait), all the Pokémon encountered have a 50% chance of having the same nature as the Synchronize Pokémon. The Pokémon that can have the Synchronize ability are the following:
*Abra *Kadabra *Alakazam *Mew *Natu *Xatu *Espeon *Umbreon *Ralts *Kirlia *Gardevoir
So first, you'll want to get a Ralts, a Natu or an Abra. Abra has a catch rate of 200 and is very rare in Emerald (route 116 and Granite Cave), so you might want to go with Ralts or Natu. Ralts has a catch rate of 235 and can be found in Route 102, but is a bit rare. Natu can be found in the Safari Zone, is uncommon and has a catch rate of 190. Remember that, the higher the catch rate, the easier that Pokemon is to catch.
To get your Natu, Ralts or Abra with the nature you want, there are three methods:
1. Breed one of them until you get one with Synchronize and with the nature you want. This can get pretty time-consuming, however.
2. If you have also access to FRLG, you can get an Abra with the right nature there easily. Just go to the Game Corner, buy 2400 or 3600 coins and get twenty or thirty Abra for 120 coins each and then check if you got the personality you wanted (if not and you don't have more money, save before “buying” them, soft reset and try again). Transfer it to Emerald afterwards.
3. You can get a Natu or Xatu in the Safari Zone in RSE (Emerald is preferred, since, if you're using RS, you then need to transfer the Pokemon to Emerald anyway) by using a rather subtle trick. Go to a patch of grass where you can find Natu or Xatu in the Safari Zone and put a PokéBlock in the feeder. It will draw Pokémon that like the flavour of that block, as follows:
Spicy: Lonely, Adamant, Naughty or Brave
Sour: Bold, Impish, Lax or Relaxed
Dry: Modest, Mild, Rash or Quiet
Bitter: Calm, Gentle, Careful or Sassy
Sweet: Timid, Hasty, Jolly or Naive
To create the PokéBlocks, using Cheri Berry, Chesto Berry, Pecha Berry, Rawst Berry or Aspear Berry is preferable for this case, since they create one-flavour PokéBlocks (one for each flavour listed above) and there are extremely easy to obtain and to harvest. After putting the PokéBlock with the necessary flavour, you'll have a higher chance of getting a Natu with the required trait (make sure it has the Synchronize ability too, however.)

Here is a list of where Ditto is located:
FireRed and LeafGreen: Routes 13, 14 and 15, in Cerulean Cave and in the Pokémon Mansion. However, Synchronize doesn’t work here, so it's not recommended to catch Ditto in FRLG.
Emerald:It is quite common in the Desert Underpass.
Diamond and Pearl: Once you've completed the Sinnoh Dex by having seen all the Pokémon native to Sinnoh, Professor Rowan will give you the PokéRadar. Head to Canalave City and buy 100 Super Repels (Max Repels are a ripoff of the highest order). Head east, onto Route 218. Stand in the middle of the grass without your bike and use one of the Super Repels, followed by the PokéRadar. Look for grass with yellow lines coming from it, and head directly for it. 18% of the time, a Ditto will appear in one of these patches. After you capture the Ditto, the grass will shake again, and you generally want to head for a patch that is furthest away, not on the edge of the patch, and has those same yellow lines. If you did it correctly, you will encounter another Ditto. This is called chaining. Also, try to level up your Synchonizer to Level 35; if you run into another Pokémon, your chain will be broken, you'll have to try again.
Now comes the important part: how to catch Ditto. We are going to consider the method to catch Ditto in Emerald here. The way to catch Ditto in DP is similar.
Go to the Desert Underpass (through Ruin Maniac's house on Route 114) with your Synchronizer equipped with the item Smoke Ball as the lead Pokémon, a low-level Magikarp, a Pokémon knowing Fly and a lot of Repeat Balls (buy in Rustboro City). The Smoke Ball is there to ensure that if the Pokémon you encounter is not Ditto, you can safely run away.
When you encounter Ditto, switch immediately for the Magikarp. The Ditto will transform to the Magikarp, and its catch rate will also change to that of the Magikarp: 255. Also, the Ditto will not be able to hurt you at all, since it will know only Splash. Now throw a Repeat Ball, and you should be able to catch it.
Another option would be to teach return to Ralts (235 catch rate) and have it attack Ditto in the turn it transforms and throw the Repeat Ball afterwards (takes less time than a switch). If you're sick of encountering level 35 Whismur, level up your Synchronizer to level 36-38, buy lot of Max Repels and use them. All Ditto are at level 38 to 45.
If you’re doing this in Emerald, after catching around 15 Ditto (or a full box), fly to the Battle Frontier IV guy (see the section 'how to discover the IVs of your Pokémon' in Part I) and let him check the Ditto you just caught. Release those that don’t have a perfect IV, change your Synchronizer to breed for another nature if you like, and repeat this process as necessary.
It actually turns out that the average amount of Ditto you need to catch in order to get six Dittos with one perfect IV, one Ditto for every stat, is 85. You might need less than this, or more, but 85 is the average number of Dittos you'll need to catch. This is slightly less than 3 full boxes of Ditto. To get these six Dittos, all with the nature you want, you’ll need to catch twice this number, or an average of 170 Dittos. You might think that 170 Dittos are a lot, but remember that you need to do this only once (it only takes a few hours) and then always use these Ditto whenever you need to breed.
Moveset Breeding
Not only IVs and natures can be passed down to the baby, but moves as well. Because of this, it is very important that before actually starting to breed, the baby's moveset should be decided, since there are some moves that can't be learned by certain Pokémon unless you breed with a particular parent. There are five types of moves that can be passed from the parents to the baby:
Level Up Moves: If both parents know the same Level Up move and the baby can learn the same move by level up, the baby will be born with that move. For example, if a male Slowbro is breeding with a female Slowking and both know the Level up move Zen Headbutt, the baby Slowpoke will be born knowing Zen Headbutt.
TM or HM moves: If the male parent knows a TM or HM move and the baby can learn that same TM or HM, the baby will be born with that move. Also, if a genderless parent knows a TM or HM move when it breeds with Ditto, the baby will be born with that TM or HM move as well. For example, if you want a Swampert that knows the move Ice Beam, and you don't have Ice Beam as a TM, you can breed your Swampert with a male Dewgong that knows Ice Beam.
Egg moves: If the male parent knows a move which the baby can only learn as an Egg move, the baby will be born with that move. You can find a list of Egg moves that each Pokémon learns on most Pokédex. For example, if you want a Sceptile that knows the move Leech Seed, you can breed a Sceptile with a male Venusaur knowing Leech Seed.
Move Tutor moves: These moves can only be passed to the baby if they are also among the Egg moves of the baby. See point 3) above. For example, if you want a Medicham with the move Ice Punch, which is an egg move, you can breed it with a male Alakazam that learned Ice Punch from the Emerald move tutor.
Volt Tackle move: When breeding for Pichu in E, if any of the parents is a Pikachu or a Raichu holding the item Light Ball, then the baby Pichu will be born knowing the move Volt Tackle.
As you can see, Level up moves and TM or HM moves are relatively easy to breed. A slight complication can occur if you're breeding for an egg move. Sometimes, you'd need to breed for various Pokémon consecutively in order to get the egg move you need. This is called a breeding move chain.
For example, suppose you need to breed a Larvitar with the egg move Dragon Dance. Checking all the Pokémon that can breed with Larvitar and that can learn Dragon Dance, we find two possibilies: Charmander and (in DP) Totodile. The problem, though, is that Dragon Dance is an egg move also for both Charmander and Totodile. So you first need to breed for a male baby Charmander or Totodile to get Dragon Dance, which would then be bred with your Larvitar to give him Dragon Dance. Charmander can breed with either Gyarados, Altaria or Dragonite, all of which learn Dragon Dance by level up, and Totodile can breed with Kingdra, which also learns Dragon Dance by level up. So there are two breeding chains:
Male Gyarados/Swablu/Dratini with Dragon Dance -> Male Charmander with Dragon Dance -> Larvitar with Dragon Dance
or (for DP):
Male Horsea with Dragon Dance -> Male Totodile with Dragon Dance -> Larvitar with Dragon Dance
Let’s give a second example. Suppose you need to breed a Snorunt with the egg move Spikes. Checking all the Pokémon that can breed with Snorunt and that can learn Spikes, we find that only Roselia can learn Spikes and can breed with Snorunt. The problem, though, is that Spikes is an egg move also for Roselia. So you first need to breed for a male baby Roselia to get Spikes, which would then be bred with your Snorunt to give him Spikes. Roselia can breed with Cacturne, and Cacturne can learn Spikes by Level up. So the breeding move chain is:
Male Cacturne with Spikes -> Male Roselia with Spikes -> Snorunt with Spikes.

The rest is covered in breeding preperations 2 since there's nit enough space for all of it in one thread!