Preparing for the Hunt
Before attempting to complete your Pokédex you will have to complete each Gym in the game and finish story mode. Travel to a Pokémart in any town and purchase ninety nine pokéballs. Swap into your team a Pokémon of low level -- it is important that while hunting and catching wild Pokémon that your Pokémon will not kill your prey in a single hit. Open you Hoenn Pokédex (it's in the menu under special items). Travel to Route 101 to begin completion.
Hunting and Catching wild Pokémon
Consult a guide for pokémon locations also consider consulting a guide for the complete list of the Hoenn Pokédex. Notice which Pokémon you are missing. Most Pokémon in the game can be found in the wild while some will have to be traded for. You will want to travel to each area of the game and hunt each wild Pokémon that you do not yet own. Remember, you can only catch a Pokémon with your Pokéball when it's health is red so in each area you will need to have a Pokémon in your party who is of an appropriate fighting level. Traveling through the wild this way will reward you with the majority of the Hoenn Pokédex.
Lileep and Anorith
A number of special Pokémon can not be caught in the wild, this includes Lileep and Anorith. To obtain Lileep and Anorith travel to Route 111 Desert and speak to the Fossil Maniac after obtaining the Go-Goggles. Then, explore the mysterious tower in the Route 112 desert to find the Root Fossil and Claw Fossil. Take these Fossils back to the Fossil Maniac to add Lileep and Anorith to your collection.
Sudowoodo
Travel to the flower shop south of Rustboro City and speak to the woman sitting on the stool. She gives you the Wailmer Pail. Take the Wailmer Pail to the south-eastern corner of the Battle Frontier near the waterfall. Here you'll find a strange looking plant on the map. Using the Pail on the plant will initiate a fight with Sudowoodo. Make sure to save before fighting Sudowoodo because you'll only have one battle to successfully catch it.
Wynaut and Beldum
If you didn't already collect the egg from the old woman in Lavaridge Town then return to Lavaridge town. You will find the old woman just below the hot springs. The egg she gives you will hatch into Wynaut. Then, return to Mossdeep City and find Steven's house. If you've completed the Elite Four sitting on Steven's table is a Beldum.
Starter Pokémon
At this point the only Pokémon you should have left to collect will require trading with friends. This means you will need a friend who also owns Pokémon Emerald. To get the other two starter Pokémon have your friend create a new game and choose a starter Pokémon besides the one you have. As soon as they finish the first part of story mode have your friend trade their starter Pokémon to you. Repeat this process until you have all three starter Pokémon.