Pokemon
¤ Red and Blue
¤ Red and Green (Japanese)
¤ Blue Version (Japanese)
¤ Yellow Version
¤ Gold and Silver
¤ Crystal Version
¤ Ruby and Sapphire
¤ Emerald Version
¤ FireRed & LeafGreen
¤ Diamond and Pearl
¤ Platinum Version

Universal Information
¤ What is this section?
¤ Breeding Pokemon
¤ Elemental Types
¤ Pokerus Infection
¤ Shiny Pokemon

Affiliates
¤ Amity Square
¤ Dark Eon Hideout
¤ Eevee's Headquarters
¤ Jenviousity
¤ Lugia's Island
¤ Perfect Absolution
¤ Pokemon Inferno
¤ Pokeshore
¤ PokeTech
¤ Pokeuniverse
¤ Pokemon Valley
¤ Sapphire Milotic
¤ The Spriting Shack

Players who pre-ordered a copy of Pokemon Colloseum received a bonus disc that contained a Level 5 Jirachi holding a Lum Berry. After completing the game, you could transfer it to your Ruby/Sapphire. I'm not sure how many times you can do this however, so if you a have a friend with this special disc, I'd would ask to borrow it and find out. There was a rumor that you could get a Shiny Zigzagoon this way also.

Deoxys was given away at events Nintendo held, or not at all.

For those of us who did not get the Special Disc or go to the event to get Deoxys/Jirachi, there is still hope. With the help of Gameshark/Action Replay, it is possible to find them in the wild and capture them. Simply head to Route 101 with one of the follow codes (+ the master codes) on and you'll find Deoxys or Jirachi after a number of battles. Thanks to loadingNOW of GameFAQs for these codes.

Jirachi on Ruby: 9BCD00D7 9222D5C8, D6E4AB8C 0B4A2B74
Jirachi on Sapp: D2B627D9 CC5D585E, D6E4AB8C 0B4A2B74

Deoxys on Ruby: 9BCD00D7 9222D5C8, B19B2D5E 4008624A
Deoxys on Sapp: D2B627D9 CC5D585E, B19B2D5E 4008624A

After entering the codes and starting your game, walk around Route 101 for awhile. They are in the route, just they act like a regular legendary would. Rare to find and capture. Please note that once capturing Deoxys, IT WILL NOT OBEY. It is only for data completion. There is not a code to make it obey you.