It really depends on where you are. Some of the attractions, particularly in EPCOT and MK, still have accessible entrances that were added after-the-fact so they don't have much choice other than sending them to the front. They are trying to mainstream as much as possible, however, which I think is wonderful - I always felt like I was taking advantage of the system when we got sent through a "shortcut." The one place I will not do the wheelchair option again was Pirates (unless it has changed), because we had to wait forever for the CM's to bring the wheelchair down to us after the ride.
This is a list of the attractions with "Mainstream Lines". These are the ones where the 'regular' line is considered to be accessible, so people using wheelchairs, etc stay in the same line as everyone else.
Attractions providing mainstream queue access include:
Magic Kingdom® Park
Ariel's Grotto
Astro Orbiter
Buzz Lightyear's Space Ranger Spin
Donald's Boat
Judge's Tent
Mickey's Country House
Mickey's PhilharMagic
Minnie's Country House
Monsters, Inc. Laugh Floor
Pirates of the Caribbean
Space Mountain®
Splash Mountain®
Stitch's Great Escape!
"The Enchanted Tiki Room Under New Management"
The Hall of Presidents
The Magic Carpets of Aladdin
The Many Adventures of Winnie the Pooh
Tomorrowland® Indy Speedway
Toontown Hall of Fame
Walt Disney's Carousel of Progress (seasonal)
Epcot®
FUTURE WORLD
Imagination!: All Attractions
Innoventions East
Innoventions West
Mission: SPACE
Test Track
The Seas with Nemo & Friends: All Attractions
The Land: All Attractions
Universe of Energy: "Ellen's Energy Adventure"
Wonders of Life: All Attractions (seasonal)
WORLD SHOWCASE
China: "Reflections of China"
France: "Impressions de France"
FriendShip Boats
Norway: Maelstrom
The American Adventure: "The American Adventure"
Disney's Hollywood Studios
Disney's Hollywood Studios Backlot Tour
Fantasmic!
Lights, Motors, Action! Extreme Stunt Show
Muppet*Vision 3D
Playhouse Disney - Live On Stage!
Rock 'n' Roller Coaster® Starring Aerosmith
Sounds Dangerous - Starring Drew Carey
Star Tours
The Great Movie Ride
The Magic of Disney Animation
"The Twilight Zone Tower of Terror"
*Voyage of the Little Mermaid
Walt Disney: One Man's Dream
Disney's Animal Kingdom® Theme Park
Caravan Stage: "Flights of Wonder"
DINOSAUR
Expedition Everest
Finding Nemo - The Musical
Grandmother Willow's Grove: "Pocahontas and Her forest friends"
It's Tough To Be A Bug
Kali River Rapids
Kilimanjaro Safaris
Lion King Theater: "Festival of the Lion King"
Maharajah Jungle Trek
Primeval Whirl
The Boneyard
TriceraTop Spin