Are these special effects limited to visual sensations?
By definition, an effect is "Something brought about by a cause or agent; a result" - Dictionary.com
Basically, it's faking an experience of some sort. In Alien Encounter, they use auditory special effects to make you think that an alien is loose in your testing chamber. They move the headrests to make it feel like the alien is right behind you.
In Horizons, they used smells to make you think that you were in an orange field. On Main Street, they use smells to make it smell like fresh-baked pastries.
And, of course, we have the visual special effects, which are the main topic of this thread.
For best overall effects, I'll go with good ol' Alien Encounter. Between the visuals, the smells, the sounds, the blood...err....water, etc. it really is the best combination of effects at WDW.
For best visual effect, I'll go with the Haunted Mansion. It still fools people today, and it still has most of the original effects.