Expedition Everest's Yeti the year it opened back when it worked the way it was originally intended to was to this day the most incredible special effect I've seen.
On the topic though, I still think that the pepper's ghost effect in the Haunted Mansion ballroom is right up there as one of my absolute favorites. Its simplicity is what makes it such an effective effect.
Of course, Tokyo Disneysea is truly the king of special effects. I think @nadroJ really nailed most of them, but I thought I'd add a few. One that is very simple but never failed to give me chills was the rain effect in Sinbad's Storybook Voyage. As you go from the first room into the second room and are beginning your "journey," there is a gust of wind and sprinkling of rain that is sent onto the riders. It's so simple, but it always put me right into the world they were trying to create. The other is way more obvious: that absolutely enormous Lava Monster in Journey to the Center of the Earth. Cause, well, it was so big!