Answer 1

The only way to obtain them legitimately is to complete the Hoenn Pokedex (after which Prof. Birch will have them in his lab) or get their evolved forms from Pokemon Colosseum (gamecube) and trade them to Emerald/Ruby/Sapphire which can be quite complicated. The easiest way to get them at this point in time is on Heartgold and Soulsilver.

Comments

However I believe that you can only do the Pokedex one in Emerald

Answer 2

Believe it or not, it's possible to get one of the Johto Starters in
Emerald. Yup, you heard me right. There's a way of getting either
Chikorita, Cyndaquil or Totodile in Emerald, WITHOUT being a dirty,
rotten cheater or trading from Colosseum.-PKMN.net

Only for Emerald sorry

For more info go here- http://pkmn.net/?action=content&page=viewpage&id=5514

For Sapphire and Ruby, sorry there is only one way - Trade from Emerald/XD

Hope this helps =P