Pokemon Box Ruby / Sapphire
While it is not part of Pokemon Emerald, there is an associated program that factors as a very useful add-on to the game called Pokemon Box Ruby / Sapphire -- more often called simply Pokemon Box. Released in North America exclusively at the New ork City Poke Center in Rockefeller Center, Box could only be obtained at the Poke Center or via its website.
This is a Nintendo Game Cube Application (often mistakenly called a game) that allows you to store up to 1,500 Pokemon in organized boxes on the Game Cube from the GBA games Pokemon Ruby, Pokemon Sapphire, Pokemon Emerald, Pokemon FireRed, and Pokemon LeafGreen.
In addition to storing Pokemon, the Trainer is offered four unique and rare Pokemon as rewards for storing certain numbers of Pokemon in the App - which they receive as eggs from the host of the App upon depositing the required number of Pokemon. These special eggs are:
(1) Swablu with the move False Swipe (Deposit 1 Pokemon)
(2) Zigzagoon with Extremespeed (Deposit 100 Pokemon)
(3) Skitty with the move Pay Day (Deposit 500 Pokemon)
(4) Pichu with the move Surf (Deposit 1,499 Pokemon)
In order to make use of Pokemon Box you must obtain the Pokedex in each game that you want to use Box with, and have saved your game at a Pokemon Centre prior to connecting it to Box. In Pokemon Emerald Trainers also need to have entered the Hall of Fame and have obtained the National Pokedex prior to being allowed to connect to Box. Trainers with Pokemon FireRed and Pokemon LeafGreen must completed the Pokemon Network Centre's Network Machine on One Island in addition to the standard requirements in order to connect to Box.
In addition to providing storage for all of your GBA version games and the opportunity to obtain Pokemon with rare move combinations, Box also serves the same function as Pokemon Colosseum in that it will repair the clock bug that afflicts Pokemon Ruby and Sapphire that can cause berries to stop growing (AKA the Berry Glitch).
Note that while you can trade and store Pokemon from all of the GBA games on the same NGC Memory Card, you can only trade them back to the game cartridge that originally deposited them. You can NOT trade your Pokemon from a game and then reset that game and trade them back. If you reset a game with Pokemon stored in Box you will lose access to those Pokemon forever.
Even with those limitations, Pokemon Box is a very useful and awesome add-on for the games. Many Trainers use it the way that I do -- to keep a perfect breeding pair of every Pokemon in the game as well as a pair of Legendaries.
-- Obtaining Pokemon Box --
Originally you could only obtain Pokemon Box from the New York City Poke Center (now known as the Nintendo World Store New York City) or through its website. Pokemon Box came with a transfer cable, manual, the disc, and a special Ruby and Sapphire colored NGC memory card with (at the time) extra storage memory in it.
If you want to obtain a copy today, your only choice is eBay, and you should expect to pay anywhere from $100 to $500 for a copy. Be warned though that the version of Pokemon Box for the Japanese Region is *still being manufactured* and is thus widely available on eBay. The problem is that it is Region-Locked, so it only works with a Japanese Game Cube! If you do not own a Japanese Game Cube you do NOT want that version -- always ask the seller if it is the Japanese version before you bid on the item. Only the North American version will work for you if you are in North America or the UK.