|Caravaggio (1986) [Ranuccio]: Throat slit by Nigel Terry after Sean confesses to murdering Tilda Swinton.
War Requiem (1989) [German Soldier]: Stabbed in the stomach with a bayonet by Nathaniel Parker after the opposing soldiers stumble across each other. There is a subsequent scene of Nathaniel meeting a bandaged Sean, but due to the film's symbolic nature and the absence of dialogue, it's ambiguous whether Sean is still alive and meeting Nathaniel in a military hospital, or whether they're both dead and meeting in the afterlife.
The Field (1990) [Tadgh McCabe]: Falls to his death from a cliff while running away from a stampeding herd of cows. (Thanks to Federica)
Lorna Doone (1990) [Carver Doone]: Drowned in a bog. (Thanks to Federica)
Clarissa (1991) [Robert Lovelace]: Stabbed to death by Sean Pertwee. (Thanks to Federica)
Tell Me That You Love Me (1991) [Gabriel Lewis]: Either commits suicide by stabbing himself or is stabbed by Judith Scott. (Thanks to Federica)
Patriot Games (1992) [Sean Miller]: Impaled through the back when he falls onto an anchor during a fight with Harrison Ford on the deck of a boat.
Scarlett (1994) [Lord Richard Fenton]: Killed (though I don't know the details). (Thanks to Federica)
GoldenEye (1995) [Alec Trevelyan]: Falls a great distance when Pierce Brosnan drops him from some equipment onto a satellite dish, then is crushed to death when the equipment crashes down onto him.
Airborne (1998) [Dave Toombs]: Killed (though I don't know the details). (Thanks to Federica)
Essex Boys (2000) [Jason Locke]: Shot in the head with a shotgun by Tom Wilkinson. (Thanks to Katy and ND)
Don't Say a Word (2001) [Patrick Koster]: Buried alive after Michael Douglas dislodges the supports to a freshly-dug grave that Sean had fallen into, causing the grave to collapse in on itself.
The Lord of the Rings: The Fellowship of the Ring (2001) [Boromir]: Shot several times with arrows during a battle with the orcs in the woods; he dies shortly afterwards while talking to Viggo Mortensen.
Equilibrium (2002) [Partridge]: Shot in the face by Christian Bale while Sean is reading a book. (Thanks to Ernesto)
Henry VIII (2003) [Robert Aske]: Killed (off-screen) by Ray Winstone's followers. (Thanks to PortsGuy)
The Island (2005) [Merrick]: Hanged when he falls from a platform during a struggle with Ewan McGregor and gets a cord tangled around his neck. (Thanks to Arnold, Gary, Neil, and Denis)
The Hitcher (2007) [John Ryder]: Shot in the head with a shotgun by Sophia Bush. (Thanks to Robert, BK, Asdrubale, and ND)
Outlaw (2007) [Bryant]: Shot in the neck and chest by police. (Thanks to ND)
Red Riding: 1974 (2009) [John Dawson]: Shot to death by Andrew Garfield, after Sean confesses to murdering three young girls. (Thanks to Brian)