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I like the Discworld system of gods...
if people believe in the power of an entity, that spirit/thing/animal gains more and more power.
So a god's career could start as an unimportant spirit of a forest or so, where something strange happens (a child gets chased by a wild animal, but for some reason the animal gives up or gets stopped), parents of the persons create a small altar (pile of stones) for the spirit, it gains power and can now more actively make people believe into it, and then gather enough followers to take over whole villages or even countries later.
Of course, in-game it would be hard to determine if someone believes into a god, let alone really believes, or is just in for the benefits (magic weapons, leader positions in cults).
But if we just have different power levels for gods whose followers win battles or handle believe like membership in a religion, the idea could be made possible. Let's assume there is a sum of mana in the whole game that is being equal to the total numbers of players (
only those count who have logged in recently), every player would "be" a potential mana point, seen from a god's point of view.
To create a god, or a cult, you will then be able to to built an altar somewhere, and name the god it is sanctified to.
You'd also define in-game things that the god values. If you name few, these might be supported more than if you name a lot.
Each characteristic could also have a negative counterpart that cannot be supported by the same god, for example a god offering resistance to Frost damage won't protect you from fire. This assures a diversity of gods, so that not everybody will be member of the same cult because it has superior stats.
Once you gain enough supporters, it will be considered an "official" god and listed somewhere in a pantheum (<- that is a greek word having to do with "all gods" basically), along with the number of members. The gods would also have an account-like database that store the characteristics and attributes: information like list of members, valued spells/stats/EXP classes/resistances/items/kingdoms/..., perhaps a description or a cult leader (think: guildmaster).
A disciple of a certain god could then force another player, who is following none or another god, to join his religion in some way -
RP, promising help, not stop killing them until they join - and now the first god will gain a mana point while the god who lost a follower will lose one. I think it would be a nice idea to hold a log of god changes, so the former cult of a player could decide to hunt him because he betrayed them.
The number of followers a god has, divided by the numbers of active players (max mana) could be used as a modifier on priest spells, or the magic effect of enchanted weapons -
which should also be made more dynamic so that they can change at runtime based on the current happenings, and only be used by followers of the same god that originally blessed them - or perhaps as a general bonus split on qualities that the god values (leucetious will not be able to give you resist bonus when no one follows him, but if he has the monopoly of followers, your electric resistance will be 100%).
These are just my personal thoughts that resulted from this post, but I like them. I wanna lead my own cult of Loriel-fanatics to destroy, uh, peace, unity and order.

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[edit] I already heared the "PARAGRAPHS!" yells ...