Unfortunately you cannot breed Flygon with any other Dragon-type Pokemon. It is the only Dragon Pokemon that can breed that is not in the Dragon egg group; instead, it is in the Bug egg group and can breed with other Bug-type Pokemon.
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Salamence learns Roost via TM. If you have used up your Roost TM, you can breed a male Pokemon of the Dragon Egg group that knows it to a female Bagon, Shelgon, or Salamence.
You can only breed pokemon, not items. Items aren't alive!
There are a number of Pokemon that can be bred in the Emerald version of the game. These include Mew and Pichu. The Pokemon must be in the same class and there must be a male and female to breed.
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That is really quite simple. All you have to do is breed a Hitmonchan or a Hitmonlee in Pokemon FireRed or LeafGreen and trade it on to Pokemon Emerald.