I have literally tons of ideas for my MMORGP, Cobalt Calibur. The governing principle of the game is that the entire world is dynamic, and entirely alterable by players. Now, this doesn't mean the game will be as rapidly changeable as, say, Minecraft, or the current state of the game. But, over time, the entire world will be able to change, either through player indirect influence, or normal activity.
There will be a lot of emergent gameplay. Perhaps certain creatures can be bred for speed, and people begin racing them.
Most games have a finite number of monsters with a finite set of AI. Cobalt Calibur will have a nearly infinite number of monsters and varying behaviors and traits, DNA, and the ability to pass features onto their children. Using Genetic Algorithms, and a natural survival of the fittest, monsters will actually learn from players how to defend themselves, like natural selection in the real world. Players will be able to breed monsters, and even keep them as pets, allowing for amazing killing machines that not even I, the game developer, could design.
Monsters will never ‘spawn' from no-where (like in every other MMO I've seen). They will reproduce and roam of their own free will. If left on their own, they will take over areas. If killed too quickly, they will die out, potentially taking their unique DNA our of the world forever. They will be able to change the landscape, for example, a cave full of spiders which have formed a lot of webbing. Once they've lived in the cave for a long time, killing them will be very hard.
There might not even be NPCs in the game, I'm not sure yet. If there are, they will have a minimal role. Perhaps, as a land owner, you can ‘hire' an NPC with certain qualifications. But, NPCs won't come from no where, they'll have to reproduce like monsters. Heck, NPCs might just be an intelligent (read as trainable) subset of Monsters.
Buildings in close proximity will form towns. There won't be any silly menus for defining towns, the game will understand what players are building.
Regions of similar characteristics, often referred to as ‘biomes' in other games, will intelligently work together.
There will be natural disasters which can change the landscape. Perhaps occasional landslides, and if your caves have been mined too much, they might collapse. This could have the effects of separating groups of players or creatures. Over time, the creatures will evolve and become unique. Players will be forced to form two separate villages.