Yes, they use different codes.
Here is GameFAQs' collection of Action Replay codes for Ruby and Sapphire:
http://db.gamefaqs.com/portable/gbadvance/file/pokemon_rs_na_gs.txt
Here is GameFAQs' collection of Gameshark codes for Ruby and Sapphire:
http://db.gamefaqs.com/portable/gbadvance/file/pokemon_rs_gs.txt
This program can generate codes for any Generation 3 game:
http://tjsdaily.blogspot.com/2011/01/ciros-pokemon-maker-download-working.html
Here is GameFAQs' collection of Action Replay codes for Emerald:
http://db.gamefaqs.com/portable/gbadvance/file/pokemon_emerald_par.txt
Here is IGN's:
http://faqs.ign.com/articles/709/709041p1.html
Here is Supercheats':
http://www.supercheats.com/gameboyadvance/pokemonemeraldcodes.htm
Here is Gamewinners':
http://www.gamewinners.com/gameshark.php?game=blgbapokemonemerald.htm