SNAFU looks like the best, as Aq suggested in Duke's link.
By level 12, you're trying to kill a target who's two miles away, on the sixth floor of a locked office building. By level 30 you'll be studying the TV watching habits of your target, realizing he watches baseball every afternoon, then sneaking onto an airfield, reprogramming a plane's flight path so that it crashes into the stadium where his favorite team is playing, the sight of which will give him a fatal heart attack.
Killchain looks like an awesome puzzle game. Quite likely the best puzzle game ever.
Besides that list?
I want an MMO with actual, complete character customization. Based on character skills you can make your own felt hat for example. If you want the brim just so, you can deform it realistically. There are no NPCs. Players own things, they want you to do things for them, and so fetch quests are basically built into the player community
by the player community.
And the dedicated RPers out there will make cool RP quests too.
High level wizards can splice animals to make horrible monsters, for various reasons. Maybe you want to make a monster with a tough hide so you can harvest it to make armor. Or maybe one with acidic blood or poisoned spittle to use for experiments. Or a weak-willed fire-resistant one to help you explore that volcano over there.
Priests are part of an organized religion, which has goals delivered to the highest priests to disseminate through the ranks. But are these high level players telling the truth of what they hear? And what if a lowly acolyte begins hearing the voice of his god and it's telling him that the high priests are wrong?
Thieves have gangs and guilds, again player-run. If a player wants to he can intimidate and take control of crime territory, but he's going to have to intimidate actual players. Will these players gather friends who can defend them from organized crime?
Do you want to pick a pocket? Just walk up and figure out what you want to take. Objects exist at all times, meaning if a player wants to put something in his backpack he must take it off, which takes the backpack object off his back and sets it on the floor. The you can open the flap and pull items out or put them in. You're limited by volume and by container weight - after all, filling a backpack with gold will make it split apart at the seams.
Or maybe you want to be a highwayman, robbing the coaches of rich merchants as they move from city to city?
Maybe you want to be one of those merchants. Or own land, and hire people to work it. You might claim a mine, hire mercenaries to defend your claim, and hire miners to mine it. You'll need to set up a supply chain where player employees will pick up the ore in wagons and bring it to the smelters, where your metal is processed and sent to your warehouse in town by another courier.
But here's the fun part: you start with nothing. The world is an untamed wonderland of natural resources, rich prairie, endless bountiful forests, and sparkling clean rivers. When the first players show up, they are members of an expedition from a dying land. They have with them only the most basic of tools, and new arrivals are shipwrecked immigrants. So what is there to do? Well:
1: There are no towns. You need some kind of shelter, right? So start making bricks from clay and sand, start making teepees from animal hides, start chopping down trees to make log cabins. Cut the sod of the prairie to make sod houses.
2: There is no economy because there are no goods. Go out and figure out how to make a bow and what to make it out of. Fish, forage, and hunt for food. Once you have shelter and food, you can get started on clothing.
3: There are no domesticated crops or animals.
4: Once you get a lot of players, you can trade goods to them for raw materials that they bring in. You can specialize, being a farmer or a carpenter.
5: We start to see trade guilds and towns develop. Maybe petty warlords gather and try to control people. There might be an uprising. You see the first eddies of the tides of history unfold and human struggles against human.
6: Scams and trickery. "Let's use my trained ferret to steal that diamond"
7: Exploration. Just to see what beautiful things are out there. To find minerals to mine and new animals to slaughter.
8: Religious organizations. Politics.
9: Your city is a bunch of stupid wooden houses on a mud road. There is no bridge over the river and a bridge would really help everyone. Can you say public works?
10: Huge monuments, tombs, etc.
11: Family lineages, robber barons, industry barons.
12: Invention of machines and magic
13: What happens to a small pond when everyone is shitting in it?
I can see the game evolve from wilderness survival to wild west, through ages of enlightenment and darkness, through graceful stone architecture, steel and concrete, and twisted post-apocalyptic wasteland. The environment would change dynamically in small patches based on what happened to this tree or that bush, so that when zoomed out to see the big picture you can watch deforestation and desertification spread. I can see the players moving through a sense of infinite resources to be exploited to environmental collapse and recovery. Or maybe they'll save themselves, who knows?
What happens when someone has their finger on the button of a fleet of nukes, and decides to press it? What if everyone dies?
Well, you see, if there's a disaster and your land is dying, you can always send out an expedition to find someplace new ...