It looks like these are the same/similar rides compared against American Disney parks. Which are different enough to ride in Japan? Which are so similar that time is best spent on other attractions?
DisneySea
Tower of Terror- Completely different than the WDW version. Like others said, you have a three point harness, but where it shines and beats the WDW version: the preshow and warehouse before loading. It is a walkthrough attraction on its own.
Toy Story Mania- Look at the outside and that's the only thing different from WDW.
Nemo & Friends- Very cute motion simulator in a huge cabin. Ride!
Indiana Jones- Very different feeling inside. Mellower colors inside as everyone is looking for the fountain of youth and the scenes are more impressive than at
Disneyland.
Tokyo Disneyland
Pirates of the Caribbean- Mix of DL and WDW. Ride.
Jungle Cruise- as others said, the skippers are all very animated and they will use you as the subject of their jokes. The ride itself was redone recently and it has some imaginative scenes and effects.
Enchanted Tiki Room. Different version with Stitch.
Country Bear Jamboree- Hee Haw! Japanese hillbillies!
Big Thunder Railway- Closer to the Paris version. It is bigger, longer than the US ones and has a pretty scene at the beginning whereas its just dark in the other version.
Splash Mountain- WDW Splash Mountain with much better pacing and bigger scenes. You don't get as wet as Florida. One word of warning: because of the 35 inches height restriction, they changed the bars to individual U bars that can be tight for Gaijins.
Snow White- Its the original WDW version pre 1994, complete with the... shocking ending.
Pinnochio- similar to DL.
Haunted Mansion- Clone of WDW pre refurbishment with small touches added. They do the Haunted Mansion Holiday Makeover here.
Philharmonic- same movie as WDW in Japanese.
Star Tours- Different waiting line and building layout. Same scenes in Japanese.
Space Mountain - it started as a clone of Disneyland Space Mountain pre 2005 refurbishment... It got its own personality in 2007.
Stitch Encounter- in Japanese only, avoid.
Buzz Lightyear Astro Blasters - Shorter than Disneyland.