Disneyland's Space Mountain is significantly better than WDW's version of the ride. How anyone can suggest otherwise is out of their mind. The WDW version is jerky and not nearly as fast as Disneyland's version.
Also, Disneyland's Pirates of the Caribbean is significantly better than WDW's version. The beginning portion at Disneyland with the Blue Bayou adds alot more character to the ride and the Disneyland version has more and better drops.
That being said, WDW's Tower of Terror is better than DCA's version. There is an opening sequence at WDW where the elevator moves along some tracks for awhile and some added scenes that you don't have at DCA. I also prefer Toy Story Mania at WDW for the simple reason that you can get fast passes there (I still don't understand why Toy Story Mania at DCA doesn't have a fast pass machine). For the same reason, I prefer WDW's version of Peter Pan (which also has a better loading mechanism giving it a greater capacity than Disneyland). The rockets are also better at WDW because they are elevated like they used to be at Disneyland (before they got moved to the entrance to Tomorrowland). As far as Jungle Cruise, Haunted Mansion, Splash Mountain and Big Thunder, I didn't notice any major differences. I enjoy both the DLR and WDW versions of these rides about the same.
Other rides that are worth comparing are DCA's California Screamin' and WDW's Rock n' Roller Coaster. Between those two, I prefer the Rock n' Roller Coaster because it has more inversions and I like the Aerosmith music involved. Also, while WDW doesn't have the Matterhorn, it does have a better snowman-themed rollercoaster in Expedition Everest. Also, while DCA has Radiator Springs Racers, WDW has a similar ride in Test Track. While Test Track seems faster, if you include the ride theming, Radiator Springs Racers is an overall better experience. Finally, while Disneyland has Indiana Jones, WDW has a ride with similar motion vehicles with a dinosaur theme appropriately called "Dinosaur." Between those two, I prefer Indiana Jones because of better theming as well.