a friend of mine Emailed this to me and i have tried it nd it works
1.) Go to the PC in the battle tower And Save works on Emerald Version only.
2.) Deposit the pokemon you want to clone in the first slot of any box Lanete's PC.
3.) Exit the computer and save your game
4.) Withdraw the pokemon from the PC that you stored in step two.
5.) Talk to the lady who takes u to link multi battle
6.) She will ask if you want to make a challenge. Select yes and choose any two eligible pokemon from your party.
7.) She will tell you that you must save the game before making a challenge and ask you if that is OK. Select yes.
8.) The game will freeze for 2-3 seconds.
9.) After the freeze it will ask u if u want to overwrte ur save file do ot press yes or no instead turn off the game.
10.) When your game is turned back on, the cloned pokemon will be both in your party and in the PC.
also u can clone items if u make the pokemon ur cloning hold the item u want to clone
i have a video of it also (its not the best but it shows u the cloning process)
There Are no SIDE effects if u do It right however if u do it wrong it could result in losing the pokemon u tried to clone so do not blame me if u do it wrong