I agree with just about everything posted here, and just about everything has been covered.
Some random thoughts:
Space Mountain at Disneyland is much better. The Michael Giacchino score is epic and truly elevates the ride into something special. The Ghost Galaxy overlay at Halloween is a fun experience as well.
I only rode Small World at WDW once, but I felt like it was completely different, but that might just be my memory playing tricks. One thing is sure - WDW's is flooded and DL's is a canal which makes for a different feel.
I refer to WDW's Pirates as '2/3 of Pirates of The Caribbean'. DL has a long bayou scene, 2 drops, a lengthy journey through caves (this is due to the space originally being prepared as a walk-through attraction. Once that was scrapped, the long caves became the ride into the new show building). Also, Disney World is missing the final scene (which is bizarre and frustrating) and I personally miss the final lift uphill, which WDW does not have.
When I rode WDW's Tower of Terror after years of riding DCA's version - I was amazed. Something happens in their version and I literally had no idea it was going to happen and it blew my mind because it was the last thing I was expecting. I don't mean to be so vague, but I don't want to ruin it.
Jungle Cruise at WDW has a really cool extra scene that makes it better in my opinion. (But does WDW have the piranha attack? I don't remember)
I personally prefer WDW's Splash Mountain. Disneyland had to work with mostly pre-existing animatronics taken out of America Sings. WDW got all new animatronics and therefore has a stronger darkride portion (although I miss the sad, singing, mamas before the drop).
HM is way better at WDW. The interactive queue is fun (in my opinion). The sound in the elevator is amazing. The library and escher scenes are cool. The hitch-hiking ghosts are incredible. (Way, way, way, different than Disneyland's version).
Big Thunder at DL is amazing now with the new track and enhanced final scene. When the darn thing works.
I don't remember WDW's Pooh for some reason.
A whole hall of Presidents is pretty nifty. At DL poor Abe has nobody to play with.
If you must compare thrill mountains, Everest is better than Matterhorn (which was recently ruined by the installation of horrendous, painful, bobsleds).
Autopia (as it should be called) is much better at DL. The entire track is lushly themed.
One point that should be made, WDW definitely has superior versions of PeopleMover, Country Bears, Circlevision, and a carousel theater show... seeing as they weren't removed.
(And in turn, Disneyland has WDW beat on Mr. Toad, Snow White, and submarines).