Ru'afo's face lift was cut down to remove some of his skin being stretched.
Picard has a disastrous attempt at a working lunch.
Riker and Troi flirt in the ship's library.
Picard and Anij kiss.
Data beams out of a buckling Cousteau.
A short discussion of the injector was removed.
Ru'afo was originally ejected into the planet's rings, growing progressively younger.
A small cameo by Quark was cut out.
Originally Riker and Troi's wedding was much longer and featured Wesley Crusher played by series star Wil Wheaton in attendance. He is still sitting next to Dr. Crusher in the theatrical version.
A private conversation between Picard and Data over a glass of wine.
Early introduction of Shinzon in the film (right after the wedding reception). This is the scene that includes the dialogue from the theatrical trailers, "But in darkness there is strength...(Viceroy)" and "The time we have dreamed of is at hand... the mighty federation will fall before us...(Shinzon)."
Worf warning Picard about the Romulans just before they leave for Romulus. This scene includes the dialogue from the trailer, "I recommend extreme caution...
Extended conversation between Picard and Crusher with Picard's old school photos.
In the original 3 hour cut Shinzon's obsession with Troi runs much deeper and there are several scenes that show him seducing and tormenting her in her mind. A scene featured in the theatrical trailers show Troi struggling with the mind meld inflicted by Shinzon and his Viceroy. You still see the effects of the tortureous mind meld in the theatrical version as Troi appears fatigued and psychologically drained.
A scene of Data teaching his brother B-4 how to eat with a fork.
A scene of Picard walking with Troi down a corridor and Troi explaining to him that he and Shinzon are two different people. This scene includes the line from the trailer, "it was like a part of me had been stolen...
Footage of Geordi and Data planning and executing the mission to rescue Picard on board the Scimitar was also cut and featured the swapping places of Data and B-4.
Sick-bay getting ready for battle, a short dialogue between Dr. Crusher and Picard is shown.
Geordi and Worf clean out Data's quarters. And Worf claims ownership of Spot.
Picard and Crusher share a final beat to close out their romance, as Crusher accepts a job at Starfleet Medical.
Riker and Troi board the USS Titan as he takes command as Captain and she resumes her job as ships' counselor.
A new First Officer is introduced on board the Enterprise and two funny moments are shown afterward. Instead of ending while the Enterprise is docked above Earth, this new ending shows the Enterprise flying away.
Perhaps Nemesis would have been better received if some of this footage was reinstated.