In Pokemon Sapphire and Ruby, Hoenn is a little different, in terms of Pokemon available to catch. Some also are slightly more common in a certain version. Here's a short list of Pokemon who are predominantly in each version (Ruby on the left, Sapphire on the right):
Zigzagoon / Poochyena
Seedot / Lotad (Exclusives)
Nuzleaf / Lombre (Exclusives)
Mawile / Sableye (Exclusives)
Wingull / Taillow
Zangoose / Seviper (Exclusives)
Solrock / Lunatone (Exclusives)
Duskull / Shuppet
Dusclops / Banette
Groudon / Kyogre (Exclusives)
I THINK this is all of them. If I missed a few, please say so!
Also, the plots are slightly different in each version.
In Ruby, Team Magma is trying to awaken Groudon so that they can control it with the Blue Orb in order to expand the landmass. Your character ends up using the Red Orb to harness it.
In Sapphire, Team Aqua is trying to awaken and control Kyogre with the Red Orb so that they can expand and raise the water levels.Your character ends up using the Blue Orb to harness it.
Also, the title screens are a little different, but I think you knew that. =P
I think that covers everything! Hope I helped!