There are no Pokemon from a Gen III game that are unobtainable in Gen IV and V games; even event Pokemon like Celebi, Mew and Jirachi have been available in Gen IV.
With the remakes HG & SS, Gen II and Gen III Pokemon have become available. Even the Kanto and Hoenn starters are available in HGSS (Oak gives the Kanto one after 16 badges and defeating Red, Steven after the same requirements and after you've met him when retrieving Copycat's doll).
Rayquaza is obtainable in HGSS as well, but you need to have both Kyogre and Groudon, meaning you need to have both HG and SS games.