I don't use a lot of undead in my games.
There are a number of reasons for this. First is the zombie issue. Zombies are among the most commonly used undead, but (I know this is sacriledge among many) I don't get excited about zombies. Zombie movies? They can be OK, but only if they aren't about the zombies. I liked 28 Days Later well enough, but I would have liked it just as well if the zombies were replaced by wild dogs or flesh-eating macaws or something. Zombies aren't interesting - it is people's reactions to them that are interesting. In most RPGs, the reactions of people to zombies is predictable. They kill the zombies. They typically do this in a manner very similar to killing other monsters. The difference? Zombies are usually less interesting than those other monsters.
Now, there are exceptions to this. One of these is when the game isn't really one in which zombies are expected. I'm currently playing in a near-future Morrow Project game (using White Wolf's newish Storytelling system). Our PCs woke from cold sleep 150 years from now to a future laid waste by nuclear and biological warfare. One of the bio-weapons had, effectively, made people into zombies. These were the first people we encountered upon waking, and - for a while - we didn't know for sure if there were any others. It was alienating and scary. Another exception is when the zombies were once people your PC knew or, with infectious zombies, if they threaten people your PC cares about. Threatening NPCs with zombiehood seems more effective than threatening them with death.
Other than zombies, vampires are possibly the most popular undead in use. The thing about vampires? Unless they are the focus of a campaign arc, the fact that they are undead is practically incidental. They are usually portrayed as acting like living people as much as possible... so I rarely see a place where making an NPC into a vampire is worth it. Couple this with the fact that I totally overdosed on vampire LARPing in the 1990s, and I just tend not to think to use them.
Mostly, I use ghost-like undead things. They give me a good deal of freedom, and I can keep them mysterious. Years of playing Wraith: The Oblivion also gave me a good pile of tricks to use when portraying ann incorporeal spirit.
D&D has its own problems with undead. Undead powers that focus on permanent debilitating effects or paralyzation just aren't fun for me as a player - so I try not to use them as a GM. Moreover, I find the 3.5 vampire and ghost templates to be mostly incoherent.
My biggest conceptual problem with D&D undead, though, is the idea of negative energy. I've never liked the idea of Positive/Healing energy and Negative/Damaging energy that work backwards on undead. It seems overly simplistic and a bit silly.
Here's another question, though. Why are undead things near-universally assumed to be evil? I like the idea of a lich who was simply a mage so infused with arcane energy that he didn't notice when he died of old age. The repentant vampire is a cliche for a reason. What about a ghoul who is driven to devour human flesh and raids cemeteries.... but hates himself for it? Non-volent zombies that are near mindless, but still try to cling to their past lives as much as they can? I could come up with some interesting scenarios around such things. Here's one: A village was infected by something that killed its inhabitants and brought them back as zombies. The zombies go through the motions of their past lives, but do so in a near-meaningless manner. Farmers go to plant seeds with empty sacks, scattering nothing over weed-filled fields. Now what if the village is in a valuable bit of real estate. Say, there's a fairly rich mine nearby. Others may want to come in a clear out the zombies - and hire the PCs to do it, not telling them that the zombies are essentially peaceful. Toss in a mystery about how the zombies came to be - and whether a recurrance of it is likely, and you have the setting for an adventure that could have some intrigue, investigation, and moral ambiguity (Need monsters? Give the zombie-flesh mutagenic properties. Animals have been feeding on the zombies and turning into half-zombie mutant things.)
Character Death and Resurrection
When I play RPGs, I see it as a collaborative storytelling experience. I don't go overboard on this, but I want a narrative that I can look back on. One consequence of this is that if a character is going to die, it should mean something. That doesn't mean that death has to be final, but it does have to be meaningful. The death of a PC shouldn't ever be trivial. That doesn't mean that a PC can't die in a trivial way (though I work to avoid that), but - if nothing else - the fact of the PC's death should have repurcussions. If the PC is resurrected, the experience of death should change her somehow. It doesn't have to be a Pet Sematary style change, but it could be a Buffy the Vampire Slayer type thing. Thinking about it, though, I think that at some point in the future I might well run a campaign where people who are resurrected sometimes come back 'wrong' - I'd totally leave it up to the player of any PC who was resurrected whether or not (or how) their PC went through something like this, though.