Well there are three most prevalent MMO themes
First one is set in medieval times with some fantasy settings usually with magic, races, and weird civilizations. Story is about world coming to an end, or it looks like it is, but then something happens, new heroes are born (you), and you struggle in a fight against evil. It seems that all is lost, but it's not thanks to you and your group in an instance
Second one is set pretty much in the same setting (swords, magic, races), but instead of you fighting with evil, you get the choice. The choice differs of course on a game but it's usually either nation, faction or side (good/evil). Story is mostly about an endless war between nations/factions/sides, but then something happens, new heroes appear (you), and you can lead your side to win.
Third one is much less common and it's hard to put it the way I put the first two. However, MMO's based on the third most prevalent theme are based on certain mythologies, beliefs or variations of these of ancient civilizations.
Examples - Gods & Heroes - Roman mythology
Mabinogi - Celtic mythology
Perfect World - Chinese mythology.
Can't think of anymore MMOs based on mythologies tho.