Any dog who's had noise/stimulation training...being exposed to lots of different noises so that they're used to it and rewarded when they do good...should be fine all all those shows. Any dog I've ever seen, my own and a couple others, rarely reacted to anything because they can't really see the screen or feel the effects. The ones I was with would sometimes perk up when they heard puffs of air or sniff if there was a scent effect but never in a distracting or bad way. We'd usually be on the end of a row or in the wheelchair row so the dog would be where a wheelchair would go. There's nothing on the floor that would interefere with a dog. I've been with a dog in Philharmagic, Muppets, ITTBAB, HISTA..I feel like I'm forgetting one...but not Captain Eo. If memory serves, the effect of the mice at HISTA was something within the seat, not by the floor.
There are not any other current 3D shows.
You may be thinking of Magic Journeys, which was the 3D show in Epcot before HISTAMINE. It moved to MK and was where Mickey's Philharmagic is now.
HISTA had some of the same general floor effects ( where the entire floor moved) as Captain EO. That was during the movie where the child picked up and moved the shrunken studio in the movie. My guess is to a dog on the floor, that would feel pretty similar to sitting on the floor for a few minutes in a moving car or van.
The other effects, as far as I know, came out of the top of the seat in front of the viewer and out of the underside of the seat you are sitting on ( the actual seat cushion, not the floor under the seat).
So, a dog sitting on the floor between seats might feel something, a dog in a wheelchair spot would feel things coming out of the seat top in front and a dog on the floor at the end of a row would only get the 'over runs'.
The back section of ITTBAB bug has wheelchair spots and also a lower ceiling than the rest of the auditorium. Some of the effects that come out of the ceiling dont come that far. The smells do, but not the spiders from the ceiling. Some of the other effects, like water, don't come that far.
The other thing we encounter every time is there will be a small child or 2 that becomes scared, cries and wants to leave. There are also screams. As was mentioned, those are people reacting to things that happen on the screen combined with what is going on in real life.
Since there are likely to be people leaving, you may want to sit in the wheelchair area or on an aisle at the show entry side rather than going all the way across the row to the exit side.
Just thought of - the one LockStoxkBarrel might be thinking of is Stitch's Great Escape. It is not a 3D movie, but has a lot of effects. Most come out of the 'restraint' harness that comes down over the shoulders. It takes place in almost total darkness at times and there are some smells and some sudden things that happen when Stitch escapes. Probably the dog will not enjoy it, but would give you some strange looks when leaving ("just WHAT was that supposed to be?"
I don't remember things coming out of the seat bottom in Stitch, but you can have the dog sit in a wheelchair spot and not have to sorry about it