Here is a list of exclusive Pokemon:
In X
Staryu/Starmie
Pinsir
Houndour/Houndoom
Poochyena/Mightyena
Aron/Lairon/Agron
Lileep/Cradily
Anorith/Armaldo
Sawk
Swirlix/Slurpuff
Clauncher/Clawitzer
Xerneas
In Y
Shellder/Cloyster
Omanyte/Omastar
Kabuto/Kabutops
Heracross
Larvitar/Pupitar/Tyranitar
Electrike/Manectric
Purrloin/Liepard
Throh
Spritzee/Aromatisse
Skrelp/Dragalge
Yvetal
Aside from the standard Pokemon, there are also some other stuff.
In single wild encounters, Zangoose and Seviper are version exclusive, but both can still be found in horde battles in either game.
Mega Evolutions: Mewtwo and Charizard both have X and Y Mega forms, so their respective stones can only be found in the version you are playing.
Some of the Mega Stones are also only found in one version (mostly the version that the Pokemon they mega evolve are in). These are:
For X: Manectrike, Pinsirite, Tyranitarite
For Y: Aggronite, Heracronite, Houndoominite
You may notice the Tyranitite and the Aggronite are switched from the versions that Tyranitar and Aggron are actually found in. I suppose it is to encourage more trading or something... Or more people buying both versions, which makes GameFreak more money... but I digress...)
To be honest, aside from he differences in Pokemon and the mega stones, I found no differences between the versions. But I have also only played Y, so there might be stuff I missed.
Sources: Bulbapedia and another question on DB
