Box Office Bomb: More in the sense of how high-profile its failure was, but it still made a fairly significant loss; its estimated production and marketing costs were supposedly in the region of $90 million, and it only made about $60 million worldwide.
Not to mention this is the only Star Trek film to not open at number one at the US box office, losing to Maid in Manhattan of all things.
Stuart Baird looked to be carving out a decent career as an action director after Executive Decision and U.S. Marshals — until the failure of Nemesis killed his directing career stone cold dead. Only his acclaimed editing job on Casino Royale (2006) a few years later prevented his Hollywood career from being killed completely (ironically, Nemesis was dwarfed by another James Bond film, Die Another Day).
Screenwriter John Logan's stock in Hollywood also dipped significantly following the failure of both this film and the same year's The Time Machine remake. Apart from The Last Samurai and The Aviator, both of which were already in production when Nemesis was released, it would be another five years before one of his screenplays were filmed.
Deleted Scene: It's been estimated that 50 minutes of footage was cut from the theatrical version. (Eight scenes were included on the DVD as extras.) Among the deleted material:
Beverly's intention to leave the Enterprise for a post at Starfleet Medical.
Wesley's cameo, in which he mentions that he'll be part of Riker's engineering crew aboard the USS Titan.
Worf saying being an ambassador (see DS9) didn't suit him.
Picard experiencing Cloning Blues, outraged there was a clone of him running around. He's talked down by Crusher.
Franchise Killer: Ultimately averted, but for the better part of a decade it looked like the Trek franchise was as good as dead, in no small part due to this movie. At the very least it killed off the TNG movie series along with almost everything TNG related (the prequel comic to the Star Trek reboot involves some of the TNG crew), and possibly even the entire 24th century branch of the franchise (including Deep Space Nine and Voyager).
Old Shame: Tom Hardy said that this film (and more specifically, the fact that it was a critical and commercial flop) was the worst thing that ever happened to him, and nearly killed his career before it got off the ground. To this day, he still refuses to talk about Nemesis in any significant detail. LeVar Burton, Marina Sirtis and Gates McFadden have also made no secret of the fact that they hate this movie.
Sirtis' segment in this video is very telling. Those being interviewed are supposed to be Selling The Show, but Sirtis can't keep her irritation with director Stuart Baird's approach under wraps. Given that her description of Baird's actions is listed as a quote for They Just Didn't Care, her annoyance is completely understandable.
Recycled Set: Averted. First Contact and Insurrection had used modified sets from Star Trek: Voyager. But VOY ended its run a year before the film was released and the sets had been scrapped. Aside from stored sets like the Bridge and Main Engineering, new sets had to be built from scratch for the Enterprise-E (ex. Sickbay). Additionally the Valdore bridge set was a redress of the Enterprise bridge.
Screwed by the Network: In two different ways. Firstly, when they installed Stuart Baird as director over any number of more qualified candidates. And secondly when they decided to release it days before The Two Towers, and with Harry Potter and the Chamber of Secrets and Die Another Day still in the midst of strong box-office runs, turning what would likely have still been an underwhelming box-office performance into one of the most notorious flops in the history of any major franchise.
Apparently, more than a third of the film (including most of the character moments and a great chunk of the expository dialogue) was cut before the final release.
The earliest version of the script was written so that Patrick Stewart would have been playing both Picard and Shinzon, and the final battle between the Enterprise and the Scimitar took place in orbit of Earth.
In addition, a later draft had the small armada waiting on the Romulan boarder joining in on the fight to have a six on one fight.
Nicholas Meyer was originally offered the director's chair, but turned it down because Rick Berman wouldn't allow him to make any serious changes to the script.
LeVar Burton was also considered as director (he had since ST:TNG directed many episodes of Star Trek: Deep Space Nine and Star Trek: Voyager, and seemed a shoo-in to be 'called up' like Jonathan Frakes had been), but Paramount went over Berman's head and installed Stuart Baird as director.
Jude Law was originally considered to play Shinzon.
Jeri Ryan was supposed to appear as Seven of Nine, but she was busy on Boston Public, so Kate Mulgrew was given the cameo appearance as Janeway instead.
Rick Berman tired to get an 11th film with a script written by Band of Brothers screenwriter Erik Jendresen off the ground, but Nemesis was such the flop it never took off, and Berman was let go by Paramount in 2006.
As late as the shooting script, the Scimitar was supposed to have its warp core on the bridge, so that Data could destroy the ship at the climax by shooting it. Technical consultant Rick Sternbach pointed out that not only was this taking No OSHA Compliance up to ridiculous levels, but Romulan starships are supposed to use different reactors which likely wouldn't go boom just by shooting them. As a result, this was changed to the somewhat less ridiculous option of sticking the thalaron beam's generator there instead.