The party is shunted to an alternate Prime Material Plane existence. This alternate reality has the same physical layout, more or less. Many of the cities are located in the same places, as are some of the major transport routes, but some cities don't exist and some new ones do, etc. This plane is a little closer to the Negative Energy Plane than the "real" plane is. As such, there are some differences in how things work for everyone except the party. (Since the party is from another plane, they acquire the Outsider type and, as such, are not affected by the change to the world.)
Positive spells are at a slight disadvantage, negative spells are at a slight advantage. For instance, cure spells are d6's instead of d8's, while inflict spells are d10's. Raise dead and such spells are more difficult to accomplish.
Undead are more prevalent and all have an additional +1 to turn resistance. "Vampire" is now a class with levels, so the lowliest vampire (level 1) is less powerful than the normal vampires; this is because on "our" realm, a vampire has to be stronger in order to even be created and in this realm, they can start weaker and grow more powerful.
Many of the typical monsters (orcs, gnolls, goblinoids, kobolds) either don't exist or are otherwise touched with negative energy (haven't worked out the template just yet). Many are replaced by other creatures that have an affinity to negative energy.
Any thoughts or comment? Something you'd expect to see in the game? Comments on how to keep the game balanced (as if 3.5 is balanced....)? Have you tried something like this before?