All shows have separate wheelchair areas. For Fantasmic, you still need to get there at least 45 minutes early as wheelchair seating fills up. Lights, Motors, Action has a lot of seats-arrive about 20 minutes before. Indiana Jones and Beauty and the Beast fill up moderately fast-30 minutes is safe, usually. The front row seats fill in faster. Festival of the Lion King is pretty popular-no later than 30 minutes. The smaller theatres like Voyage of the Little Mermaid and all the 3D shows often give return times because the wheelchair seats are taken for the other shows. Especially for these shows, go to the wheelchair line with the gate and wheelchair symbol so if the show is full for wheelchairs you get a return time. The Tiki Room and Country Bear Jamboree and Flights of Wonder also have fewer seats but aren't as popular so seating generally isn't a problem. Now for the wheelchair parade seating, especially Spectromagic, you really need to get there about an hour early if you want the front row seat. Even the second row is usually filled 20 minutes before the parade.
I think that about covers all the ones I know of. A note on Indiana Jones-FP is pointless because there is only one wheelchair line.
-Christamae