I think one of the biggest things here is flexibility. It's been said a few times already in this thread and in my experience it routinely separates the games I enjoyed from the games I did not, on both sides of the table.
I have actually introduced a thing where I spontaneously hand out XP (A free skill point or a few FATE points usually) to any player who completely throws me off with the creativity of their solutions. The other DMs I play with have picked it up too. Last time I recieved one was in a DnD game where I used an unconcious (but not yet dead) beholder as an antimagic gun. (The big eye still works until it actually dies!) Completely broke the encounter, but the DM was totally cool with it and had some badguys retreat because their magic didn't work.
I'm a very character driven writer, so my method usually involved writing the campaign as if my NPCs were PC. What is their longterm plan? what do they have to do to pull it off? what are the environments they'll be doing them in? What's their timetable? Who is the most critical in various areas?
Then when the players stumble into it I have solid objectives for my NPCs regardless of how the characters may interfere with their plots. It gives both sides of the encounter equal narrative momentum and importance, without making the game into a railroad.
Example:The NPCs really want to assemble the Seven Shards of the Heavens to summon an outer god. The shards are in various temples scattered around the world undeground, except for one which is the Louvre as part of a larger scupture. They plan to gather the seven seperately, ending with the Louvre one since it's actually harder to find the current location of than the ones still in the temples.
This is a nice broad storyline that would work equally well as a PC based adventure, which in my mind is the hallmark of a convincing evil scheme.
If for example, the players get to a shard first, or show up at the same time, we now have an encounter between those NPCs and the players. Perhaps the NPCs now attack the players at their home base to recover the shard, or try and trick them into using it as part of their ritual. Maybe the players don't even take interest in this plotline! That's cool, it'll still happen and they'll have to deal with the summoning ritual directly later which is a pretty cool adventure/encounter on its own. Or maybe they NEVER get involved, and some other group of heroes deals with it, or the Gods get summoned and start their dominion over the earth. Look ma, new BBEGs!
I played in a game where this was done rather expertly in that there was a civil war brewing between two factions (I think it was some halflings and some humans) and he was trying to get us involved in it. We didn't bite, and went off questing after a magic gem. When we got back the war had broken out, and we had to help settle it before we could recieve our reward for getting the gem. Good times and really helped create the feeling of a real world.