Catch pokemon by weakening them (all except for the level 20 Remeraid) then throwing any pokeball (except for masterball save this one for last). I have 42 pokemon.
Sent in by Jeff Bormann

saving balls (i know is sounds ronge):

This is more like a hint in a glitch in the game. use a ball on your first turn and then switch it on your second turn it works all the time.
Sent in by: jason

Entei ~.~ When you get to Mt. Battle and battle to the top, you will face Cipher Admin Dokim. He has Entei as a Shadow Pokemon.

Ho-Oh ~.~ To get Ho-Oh, purify all 48 Shadow Pokemon and defeat 100 trainers on Mt. Battle using only the Pokemon from your story mode team. Note ~.~ Your PC must have an empty slot.

Jurachi ~.~ To get Jurachi, load him into the Game Boy Advance from the bonus disc. Then, transfer him to Pokemon Colosseum.

Raikou ~.~ Raikou can be found as a Shadow Pokemon of Cipher Admin Ean in the Shadow Pokemon Lab.

Suicune ~.~ Suicune can be found as a Shadow Pokemon of Cipher Admin Venus in The Under.

Togetic ~.~ Defeat the Deep King Agnol in the Deep Colosseum. If you have all the Shadow Pokemon you will get a message about someone attacking people with a Shadow Togetic. Rush to the Outskirt Stand and fight him.

Tyranitar ~.~ This is the strongest Shadow Pokemon in the game. You only have one attempt at this, so use the Master Ball. The leader of Cipher has it.

Croconaw, Bayleff and Quilava ~.~ After getting one starter Shadow Pokemon at the beginning, you need to get the rest of them. Complete the game and go to the Snagem Hideout. Look through the hideout until you see a man in only one color (green, blue or red). Battle him and snag his Shadow Pokemon. You will soon get an email. When you get it, go to the Kids Guild and talk to Nett. Then, go by the Junk Shop and fight Gurks. Talk to Gurks then go to the Shadow Pokemon Lab. Go to the last room of the Lab (where you fought Ein). You will see a person. Battle him and snag his Shadow Pokemon.

Catching the Legendary dogs ~.~ All three Legendary dogs (Entei, Suicune, and Raikou) are best caught with Ultra Balls, but it possible to do it with Great Balls.

Amulet Coin ~.~ Successfully complete the game, then go to the Deep Colosseum. You will find Silver Teeth as you are about to enter. Go to the old man outside the herb shop. Give them to him, he will give you UFO Disk -L. This will enable you to go left and get the Amulet Coin. The Amulet Coin gives you more money when you use the Pokemon equipped with it in battle.

Badges ~.~ Defeat Mirror B (Red Badge), Dakim (Green Badge), Venus (Blue Badge), and Ein (Yellow Badge). Use all the badges to open the door in the Realgam Tower. You will also get them at the Tower.

Cologne Case ~.~ A girl east of the Pokemon Center in Agate Village will give it to you. She is in blue clothes. Answer "No" to her in order to get it.

Coupons ~.~ Battle at Mt. Battle and clear an area. Go inside a metal box at the end and talk to the lady. She will give you Coupons. The more areas you clear, the more Coupons you will get.

Disks:

F-Disk ~.~ Defeat Dakim at Mt. Battle.
R-Disk ~.~ From the kid locked up in the cage, in the Under.
U-Disk ~.~ In a chest, in the Subway, near the boxes.
D-Disk ~.~ Defeat Head Gonzap in the Snagem Hideout.
L-Disk ~.~ Talk to the old man in front of the Herb Shop.

Exp. Share ~.~ Go behind Eagun's house and down the slope. You will find a chest containing an Exp. Share.

Master Ball ~.~ After you have the badges you will get an email from Eagun. Go to him in Agate Village. Talk to him and you will receive a Master Ball.

Strategy Memo ~.~ Go to the Pre-Gym and talk to the teacher to get the Strategy Memo. You can always update your Strategy Memo by talking to the teacher again.

Time Flutes ~.~ The first Time Flute is obtained after you defeat Dakim. The second Time Flute is obtained when you put the U-Disk in the UFO (it is in a chest in the room).

A third Time Flute can be found on the 100th Mt. Battle area. In order to get it, you must have at least level 60 Pokemon.

Trade Machine ~.~ Defeat all the opponents at Realgam's Colosseum to unlock Trade Machine to transfer Pokemon to and from Pokemon Ruby and Sapphire.
Successfully complete the game then go to the Pokemon Center in Pheanic town. Go downstairs and talk to the woman. You will now able to transfer Pokemon from your game to Pokemon Ruby and Sapphire and vice-versa.

Deep Colosseum ~.~ Use the D-Disk on the UFO to get to the Deep Colosseum.

Deep King Agnol ~.~ Complete the Deep Colosseum four times. On the fifth time you should fight Deep King Agnol in the last match.

Ein's Lab ~.~ To get the code for the locked door in Ein's Lab, get all three DNA samples and identify them all with the DNA machine inside one of the rooms in the lab.

Herb Shop ~.~ Use the F-Disk on the UFO. Instead of going in the Under Colosseum go left and up to find a Herb Shop.

Orre Colosseum ~.~ Get through the Phenac Stadium, Pyrite Colosseum, and Under Colosseum in single and double battle modes to unlock the level 50 Orre Colosseum. Get through the Tower Colosseum in single and double battle modes to unlock the level 100 Orre Colosseum.

Team Snagem Hideout ~.~ Successfully complete the game and go to Pyrite Town. Go inside the secret passage by the bookshelf. Talk to one of the kids and fight Cail (the person with the green hair that hangs out near the entrance of Pyrite Town). After you win the battle, talk to Cail. The map will now show the Snagem Hideout.

Team Snagem's hideout (the one you blew up in the beginning) has many trainers and some good items.

Purify quickly ~.~ Get the Time Flute and call Celebi. When Shadow Pokemon see Celebi, they will become purified. Alternately, get the Time Flute to Jurachi to do the job.

Restore health ~.~ Use the following trick at a save point to restore your Pokemon to full health. Put the fainted Pokemon in, then take it out again.

Easy money ~.~ Successfully complete the game then trade your Pokemon back and forth from Pokemon Ruby or Sapphire. Give the trading Pokemon Nuggets then sell them in Pokemon Colosseum. This can also be done with other items.
Sent in by Tim Shore