Main Street/Castle
The WDW versions are both much large. This is great for visual effect, but the intimacy of Disneyland's is a plus. Main Street at Disneyland still has a unique feel to it with each shop offering a different type of merchandise for the most part (this is starting to disappear, but its sort of still there). WDW on the other hand felt like a mall to me after a while. Especially with the new enlarged Emporium.

Believe, there's Magic in the Stars vs. Fantasy in the Sky
Believe is much better. The music and effects are incredible still even after seeing the show dozens of times. Fantasy in the Sky has some large effects and the Castle is extremely impressive, but the sound track just does not do it for me. Seeing Tinkerbell fly by the castle is better to me than seeing her fly out of the castle.

Peter Pan, Small World, Snow White's Scary Adventure
The first thing you will notice about these three Fantasyland attractions is that the facades @ Disneyland are much more impressive in detail and scale. The WDW versions are very plain and dare I say boring. The interiors are very similiar. Small World is the biggest difference. At Disneyland it has an exposed canel, where as at WDW it is level with the sets. The sets also seem more elaborate at Disneyland. I would give the edge to Disneyland's versions of the attractions.

Pirates of the Carribean
Disneyland's version of the attraction is much better in my opinion. The length, two waterfalls, extended caves, and reverse waterfall but it over the top. The queue area and facade are better at WDW, the old fort is impressive, but the ride itself just can't compare.

Jungle Cruise
This was pretty much a draw. The WDW version has the "ruins", but the classic Disneyland is still great.

Haunted Mansion
This one is also a draw. WDW exterior is much more impressive, but the way Disneyland's is set up I like better. The true elevator makes the stretching room effect better in my mind. I also like walking through the hall of portraits and the "head" effect. The main part of the ride through is very similiar. I also like at Disneyland how you have to ride up the speed ramp and the little Leota is there talking to you. At WDW I like how you have to walk by the graveyard so you get to read some of the tombstones, where as at Disneyland you by bass it almost all the time (especially now with FastPass).

Tea Cups, Dumbo, Carrosel
All a draw. Pretty much the same both places.

Tiki Room
I am a sucker for the classics so I like the original at Disneyland better. Also I do not like the Under New Management skit at WDW. It just did not seem interesting/funny to me.

Autopia
The new version of this at Disneyland is the better. The variety of cars and additions to the track at Disneyland put it over the top. At WDW its a very "boring" track. Some of the Indy theming is cool at WDW, but overall Disneyland is better.

Disneyland RR vs. Walt Disney World RR
This is a tricky comparison. The large trains and the longer route at WDW are great, but the additional stops at Disneyland are also a plus. I enjoy both of them. I like WDWs because you get out to what feels like real wilderness. But Disneyland's acts as a much better transporation methode.

Swiss Family Treehouse vs. Tarzan's Treehouse
The WDW Swiss Family Treehouse is much more impressive to look at, but I think more kids can relate to the Tarzan version. So its pretty much a draw.

Monorail
The edge here definetely goes to WDW. The monorail is actually an essential mode of transportation. Its great to use to get around. Where as at Disneyland its still mostly an attraction. Yes you can use to to get to Downtown Disney and back, but how many people actually do that...

Innoventions
WDW's version is much better. For one thing you can get straight to the exhibits and do not have to watch the same Tom Morrow clip over and over and over again. Also it seems to have more cutting edge technologies. I know having more space and a less constraining building really helps to put EPCOT's version over the top. Also I think its gotten so much better since the large video game section has shrunk.

Space Mountain, Splash Mountain, Big Thunder Mountain
The three Mountains are much more impressive at WDW. Having more land really makes the facades much large and more interesting. The rides themselves have mixed reactions from thrill seekers, which I am not.

Star Tours
Exactly the same film/simulator experience. The building at the studios is more impressive to me because of the forest set outside.

Tom Sawyer Island
Another tough choice. I think WDW has the edge because it is large and has more caves to explore.

Mark Twain vs. Liberty Belle
The Mark Twain impressed me more. The ride experience is pretty much the same in terms of going around the river and seeing the sites. WDW feels more like your in the backwoods to me.

Fantasmic
Disneyland's version is much better in my mind. The show relies much less on video and more on live action. The Peter Pan segment on the Columbia is much better than the Pocahantos segment in WDW. The finale of the Mark Twain steaming around the river is much more impressive than the Steamboat Willie boat used at the Studios. Yes almost every seat in Florida has an unobstructed view, but I really like watching NOS being transformed into a theater everynight. Its still hard to believe the show is 10 years old at Disneyland (debuted May 1992).

Kali River Rapids vs. Grizzly River Run
They are both extremely well themed river adventures. I have to give the edge to GRR in terms of overall ride experience, but to Kali in terms of theming. GRR seems a bit longer and the larger lift hill and two drops add to the experience. Kali on the other hand gets you much wetter (which may or may not be a good thing). The "jungle" that Kali goes through is visually interesting and great. One other advantage GRR has is Free lockers near by to store your items in.

Maholland Madness vs. Primevial Whirl
These two attractions are quite different, but both are "Mad Mouse" designs. I did not get on Primevial Whirl (due to my lunch timing). So this comparison will only be observations. Whirl seems to be a little better because you get to spin as you go through, but MM seems tighter and faster.

Indiana Jones Adventure vs. Dinosaur
Indy beats Dino hands down. The overall theme of the attraction is so much better. Dinosaur is an interesting ride, but most of it takes place in the dark and its just not that much fun. Compared to Indy where you see almost everything and experience several different areas.

Muppets, Tough to Be a Bug, Honey I Shrunk the Audience vs... themselves
These three 3D movies are the same in both parks. Some of the theater effects are slightly different but the overall experience is pretty much the same. The buildings in WDW are much more impressive from the outside, but inside are very much the same. If you have seen them in one place seeing them in the other is for the most part the same experience so you can use your time better elsewhere probably.