I developed this "shtick" in my d20 Modern campaign, but I have since carried it over into other genres because it works so well:
Every adventure I write is basically 2 adventures merged into 1. I take 2 "threats", each with their own appropriate goal or motivation, and find some way to link them, and unleash them both on the PC's at the same time. The result is that the adventures honestly seem to write themselves, with a lot less work for the DM both in pre-planning and in at-the-table improvisation.
For example, generic fantasy campaign, in a large human town. Let's say you have some lizardfolk secretly living in the sewers. We'll have a new young human vampire in the sewers who is stalking the local lizardfolk and creating vampire spawn lizardfolk down there in his bid to take over the city from the older vampire currently living in the area.
Now, for a second villain, let's say we have a rich merchant who has paid thieves to steal certain gem-encrusted relics of an old saint from the town's churches because his daughter is possessed by an evil spirit. The spirit has told the merchant that he will leave the girl's body if the merchant gathers the relics and sacrifices them to the spirit. The "spirit" is actually a psionic mindworm parasite that recognized the gems as psionic crystals. The mindworm can also control several of the merchant's house guards and servants.
Connections between the two adventures: The vampire was once in love with the merchant's daughter, back when he was human. The lizardfolk have a small secret temple in the sewers, which houses one of the local relics that the mindworm needs. The mindworm is ancient, and knew the vampire's sire. The vampire may conduct a theft of his own, to steal the holy water font from the local cathedral, knowing that it will look like the other robberies and not be tracked back to him. Maybe one or maybe all of these links are true, maybe there are others.
Okay, now, enter the PC's. They get attacked by some vampire lizardfolk, and they realize there is a threat. Stories spread around town of children or livestock disappearing. Meanwhile, the clerics in town spread the alarm because their relics are vanishing in daring midnight robberies. Are the two connected? If so, how? If not, what is going on?
Advantages to this method:
1) It almost never bogs down. If the PC's get stuck trying to unravel one plot, you can just hit them with something from the other plot. Jump back and forth whenever the action slows down.
2) It makes both plots seem more complex and conspiratorial. You get a lot of "okay, so what does this have to do with the other thing?" Sometimes the ideas the players come up with are even better than your own original ideas, in which case you can switch over to their idea. Really simple mysteries can be made to seem much more convoluted because they are happening simultaneously.
3) It lets you force tough moral decisions. Occasionally the PC's will be forced to let one villain go in order to stop the other one, or find themselves in other similar moral quandaries. Great for roleplaying.
4) It lets you play with disparate elements in the same adventure. In this one we have a vampire coupled with a freaky mind-worm and a series of robberies. The more different the two plots are, the better.
5) It lets you balance combat and roleplaying encounters with ease. One of the two plots could be entirely combat-related, and the other could be entirely about roleplaying, and it feels like one complete adventure that runs the spectrum.
Disadvantages to this method:
1) Red herrings work a little too well. When you have one mystery to solve, you can sometimes tell when you are given a red herring, and you know not to follow it. When you have 2 simultaneous mysteries to solve, anything could be a clue, so you will spend some time running down false leads or finding subtle ways to indicate when a particular track is going nowhere.
2) You need good note-takers. The players will often have multiple leads that they want to track down, and after finishing one, they might not remember what else they wanted to do.
3) Players who are really used to the BBEG template adventures can be very confused and refuse to accept the realization that there are 2 simultaneous unconnected villains operating in the area and may spend an inordinate amount of time looking for the 3rd BBEG who is behind them both.
In this sample, the PC's might stake out the next temple to get robbed, or they might question the locals to find out the pattern in the childrens' disappearances and see how they are all near sewer entrances, or they may track the lizardfolk back to the sewers or they may try to join the local thieves guild to see who put a contract out for the relics. Research into the relics might reveal that the gemstones in the relics could be used as food for a mindworm. In between gathering clues, you can hit them with lizardfolk ambushes or criminal guild hit squads trying to silence them before they get too close or psionically controlled town guiards and other warrior types, plus any other combat or trap encounters along the way. They might end up eventually getting approached by the non-vampire lizardfolk who want help, or they may get paid by the enraged town council into eliminating *all* the lizardfolk, vampire or not. Finally, you get a dungeon-crawl to eliminate the sewer vamp and his minions, and then a showdown with the mindworm and guards in the merchant's house.
