subplots
I have a quite a few subplots running ... or maybe they should be called "background archplots". There is not real "main plot", just different adventures, but each adventure provides clues to one or more of several major galaxy wide events going on, and it's not always clear which clues are for which plots. It's been kind of subtle, but i warned the players to pay attention to small details and they are just starting to see some patterns. It's kind of fun watching it happen.
I'm running dragonstar, but most the plots could be adapted to normal fantasy dnd. One major plot is that Doppelgangers have been sort of wiped out and most people have never heard of them or know anything about them. Many thousands of years ago they were systematically hunted down and killed. But of course some survived, and now they are slowly growing in power. They are organized across the universe and some are highly skilled and they are slowly but surely replacing key powerful figures planning to take over the universe. They have appeared in the middle of the most random adventures ... little clues here and there. For example, they were up against some armed bad guys in a supply station when they found one of hte bad guys naked and dead and shoved in a closet. It was weird but at the time they didn't think too much about it. A doppelganger had replaced that one. He managed to escape to they never figured out much, but had that clue anyway for later.
Another major subplot is that there is a threat from a great undead army run by a powerful vampire. They have been beaten back for now, but are always a serious threat. An important thing in my campaign is NOTHING is random. If you open a door and see a monster you need to be asking "why is that monsters in this room, how did it get here, what is it doing here?". So when the group ran into undead randomly appearing several times in weird places they new something was up. This seemed to coincide with the appearance of a new drug called "Flash" that was some sort of stimulant. They now suspec that the drug turns adicts into undead and it is a plot by the undead army. They had early on found a clue about a place where a merchant was going to make a large purchase of flash so now they are heading there to see if they can track down the source.
Another subplot has to do with psionic police. In my campaign psionics are illegal ... you have to join the "Psicore" or die .. or go into hiding. One of the characters is a psion and has to be really really careful. Anyway, they've randomly seen these strange tatooes which they think are psicore members, but there have been two different types of similar tatooes. Right now they think they are different ranks, but in reality one is an ex group of psionic drow working together to unite the drow to overthrow the dragon rulers and take their rightful place at the top of hierarchy.
There are a few other subplots going on, but I hope this gives you guys some ideas.
I'd like to hear other people's ideas on subplots since I think they really add a nice dimension to the campaign if done well.