I've never liked the perception of undead-as-evil. They're disgusting, horrid, repulsive, all those other words that say that the use of zombies as manual labor will probably never be acceptable except maybe where the living wouldn't want to work anyway (piling up and burning plague victims, etc), but not evil.
Negative energy isn't evil. It's not against the "natural order of things," a phrase that always annoys me. Decay is a natural part of the cycle. Break things down to make new things with them.
In my settings, the perception of evil spirits is a side effect of the way Styx (the plane of death, negative energy, etc) interacts with Mundum, the Material Plane equivalent. Souls of the dead have a natural tendency to return to the 'echo' of either the place they died or some other familiar location. They perceive Mundum through a sort of veil, obscuring many things from them. So when some idiot wanders into what they still consider their home or worse, starts looting it, they tend to get pissed off. Enough of these encounters and spirits have a reputation for being crazed and vengeful.
Zombies and skeletons are, as mentioned before here, essentially puppets. Disgusting, smelly, and often leaking various decaying fluids, but still just puppets.
Liches and mummies are intelligent, but nonevil, undead. Mummies tend towards Lawful Neutral actually, usually created for the purpose of eternal guardianship. Liches are just people who figured out how to lock their soul in a box. Ghouls and Vampires are the worrisome ones. Both were originally created by evil gods, and need to constantly battle their base urges.
Ghouls were created by a God of Murder as essentially zombies with the soul shoved back into it. Most of the reputation of undead being EVIL and not just "unnatural" comes from them, ravenous, murderous beasts that want to bite your face off for no other reason than that it feels good. Obviously some can fight it, but few do.
Vampires were created by a God of Avarice, which goes a long way to explain their common 'man of wealth and taste' persona. They aren't evil, per say, just always thirsty, and have a tendency to horde wealth much as dragons are prone to (unsurprisingly, the God of Avarice in question was a dragon god). Vampires have a better reputation than ghouls in that sense, and so long as they keep playing the role of the reclusive nobleman in his mountain estate, nobody's gonna grab the torches and pitchforks.
Since I don't want to bring it up every thread I'm in, my games only allow material from books I have physical copies of. I do not use the SRD.