Okay...
1) Why? Answers that jump to mind.
Bad Luck - This is a catch all. It involves really bad luck. Someone gets hit in the head with a meteor. Your PC's favorite Ultimate Weapon fell out of his pocket. There is usually no one behind it, it's just an accident. However, the PC may not KNOW there's no one behind it, and several red herrings can lead him to believe it was anyone from his arch rival to the paper boy.
Bug Hunt - Pick something to be the Bug. Have the players hunt and kill it.
Conspiracy - Two or more antagonists get together and do something to threaten the PCs. The PCs are typically the enemy of the status quo. Those in charge hate change.
Escape - Confine the players in a dangerous situation. Let them try to get free. This could range from escape from a city, the undead, or madness.
Rescue - The counterpart to escape. Someone else is stuck and the PC's need to go in and get them.
Siege - Many, Many, Many low level scum to die in droves.
2) Mood? You got three answers here.
Grim - Life sucks, it's always raining, and you got a hole in your shoe. Nothing has any color. Stack the cards against the players, but only in a cosmetic sense. Things end poorly UNLESS the players work hard to make sure it doesn't.
Horror - Beyond grim, there is Horror. The PCs have a slight chance to win, but if they break even, they should be happy. Evil is out there; it's older, more powerful, and its got the edge. Big Evil is typical and frequently the players Cannot Win. But, they can hold off the coming of the Final Night. They can hold out another day, and where there is life, there is hope. Tentacles are a must.
Unrelenting Nastiness - Ewwwww... Hit the player's right off the bat, HARD. Keep them off balance. Deplete their resources, nickel and dime them to death. Everybody is evil. Your old school teacher you liked so much? He's in jail for being a cannibal. They can't win. They can't break even. They can't quit the game. BUT, they can get a Pyrric victory. They just might be able to take the bad guy with them. The best the players should hope for is to make sure Nobody Wins and that they get out Alive. Usually, it's one or the other. NOTE: Most players will hate you, they came to have FUN and relax - not to struggle this hard. Find out if this is their kind of fun BEFORE you run it.
3) Theme? Got some suggestions here:
Foreshadowing - This is basically when you include something in the adventure eerily on that tells the players what might happen in the future. I'd have the stars move around alot and make wierd shapes all the time as the necromatic energies of the world shift around.
Symbolism - This is where you use symbols to represent things. Pick some shapes to keep popping up. Don't worry what they mean, the players will start to speculate. Take the idea that works best for you.
Personification - Since the living is becoming partially dead, make inanimate objects partially alive. Give inanimate objects a human quality. Describe rocks as squatting, or old buildings as hulking. Objects should be described as doing or feeling something. They should not actually be alive, but the goal is to have a world being overrun by undead, so too shall the inanimate start to take on animate qualities.
4) Incentives, or Why should the PCs give a shit?
Knowledge and Power. Give out knowledge with an eyedropper, but be kinda liberal with the power. Supplies are a form of power. Magic even more so.
5) Events at the base of operations
Friendly Forces - Friendly forces to the player show up and offer to help the players, want the player's help, or maybe they just want to hang. Or maybe they've had mind control devices planted in their heads and are waiting for the right moment to have their brains detach for their spines and flail tentacles around and ... and ...
New Supplies - For what ever reason, the players get fresh supplies of Magic, money, lawyers, Food, whatever. Either they stumble across it or someone gives it to them.
Opportunity for Profit - An opportunity for profit that has nothing to do with the current conflict presents itself. A neutral third party wants help getting the shipment of Y to X, for example
Opportunity for Treachery - Someone gives the players an opportunity to do a Benedict Arnold. They offer the players a lot to change sides, look the other way, or in general make a profit at the cost of their side.
Raiders - Someone wants to take advantage of the chaos and a third party comes in to attack. The third party is looking for profit and then wants to bug out.
Actual encounters
Ghoul Babies. Nuff said.
Someone is stealing locks of hair from the PCs as they sleep.
Someone offers a PC 100 gp to blow over a glass of green fluid, but refuses to explain why.
The king offers to pay them large sums of money to work for him, but starts to tax the crap out of money they make adventuring. The goal is to make it so they are dependent on him.
They find the animate corpse of a childhood hero of one of the PCs.
Some of the undead try to talk to one PC and repeatedly ask why he is with the "warm ones." He just happens to look like one of the evil necromancers.
Nightmares. Lots and Lots of nightmares.
A baby winds up at the PC's home with a note: "Don't let them get her. There isn't much time."
A vampire falls in love with a PC. Hackney, I know. But hey. Go with the classics sometimes, ya know?
The PC is reading at home when the book bursts into flames and the walls start bleeding. A thousand voices start chanting in Faux Latin. If the PC speaks Faux Latin they are saying "He is coming. Prepare the way!" Then the flames and blood goes away
The Leaf Wight. A powerful, yet OCD, Druid dies in his sleep and comes back obsessed with lawn care. Woe be to any with poor landscaping skills.
Someone thinks the PCs are undead, but hiding it very well. Nobody believes them. Every once in a while, the PCs find burning chicken skulls outside their homes. It's a way to ward off demons. It doesn't work. He's just bat shit insane.
And my personal favorate: People are suddenly grasping their heads, falling to their knees, then teir skulls pop open. Their brains (with eyes still attached on stalks) sprout nerve ending tenticals and run off, trying to get into the sewer. They are all gathering together to form a horrible undead brain-thingie with a thousand unblinking eyes. The longer it takes to stop them, the bigger it gets until it eats the city. Evil sewer necromancer a must.