This is a list of all the people who die in the books Dune and Dune Messiah (and the rest later) by Frank Herbert. It is meant to be an exhaustive list so if I've forgotten anyone please /msg me to let me know. The page numbers are from the edition that I own and so are only a guide unless you own the same one (It is a New English Library edition purchased in about 1995. It is the edition with the full cover art.)
Be warned this write up contains many, many spoilers.
The book Dune is divided into three sub-books: Dune, Muad'dib and The Prophet.
Dune
p93, Harkonnen Hunter Seeker operator.
He is the operator of the floating needle that is hidden in the headboard of a room in the keep at Arakeen. The room is made to specifically attract Paul's childish nature. The hunter seeker nearly kills Paul but he deals with it. Thufir Hawat's men say about the Harkonnen agent that they, 'messed up catching him'. He is the first person to die in the book.
p111, 259 key personnel, 100 remaining.
In a meeting Hawat discusses with the Duke the measures they have taken to gain control of the commerce of Dune. These Harkonnen sympathisers are assassinated or marked for assassination by Hawat's people.
p112, Harkonnen mercenaries disguised as Fremen.
They are killed by Turok, a courier for the Fremen. Stilgar intrudes on Duke Leto's meeting to claim Turok's water. He lets the Duke keep it after Duncan Idaho signs up for a dual allegiance with the Fremen and the Atreides.
p120, Harkonnen Messenger with letter about Jessica.
Mentioned by Thufir Hawat when he warns the Duke about Jessica. He was intercepted. The note speaks of a traitor called Pardee who is assumed to be Jessica, the Duke's concubine.
p188, The Shadout Mapes.
Killed by Dr. Yueh to attract the Duke's attention so Yueh can inject him with tranquilisers before the Harkonnen attack.
p201, Kinet, Czigo, Scarface (deaf).
These three are the Harkonnen unfortunates that take Paul and Jessica to the Desert in the ornithopter. Jessica uses "the voice" to make Czigo to kill the other two and then cut Paul's bonds. Paul kicks him in the chest, killing him.
p207, Atreides trapped in caves or killed by Sardaukar.
The Harkonnen (Sardaukar) artillery traps many Atreides soldiers in the caves of the Shield Wall. Many others are killed in battle.
p208, Dr. Wellington Yueh.
Stabbed by Piter deVries in the back so he can join Wanna his wife. A fitting end.
p214-215, Piter deVries and Umman Kudu the guard captain.
These two are gassed by Duke Leto's false tooth. The Baron was the actual target but narrowly escapes because he was wearing a shield which slowed the diffusion of the poison gas.
p216, Duke Leto I.
Dies due to the above gas. The first of three suicides in the book.
Muad'dib
p248, Two Fremen and 100 Sardaukar.
A conversation between Thufir Hawat and a Fremen. Thufir is amazed that they managed to kill so many Sardaukar with so few losses.
p249, Arkie.
Atreides soldier who dies, and is taken away by the Fremen as a water bond between Hawat's men and the Fremen.
p252, Eight Sardaukar.
Five Sardaukar on the ground and three in an ornithopter that foolishly lands near a group of Fremen.
p253, Sardaukar troop carrier (estimated 300 men) and one Fremen.
The above thopter is crashed at great speed into a Sardaukar troop carrier by the Fremen pilot. "A reasonable exchange". Second of the three suicides.
p254, One Fremen
The Fremen who Hawat made the water bond with (p249) is hit in the throat by a Sardaukar knife.
p262, Duncan Idaho.
Duncan Idaho and Liet Kynes find Paul and Jessica in the desert. The Sardaukar follow. Idaho dies buying Paul and Jessica time to escape in a stolen ornithopter.
p301, Mattai.
Gurney Halleck leads a group of Atreides soldiers to the smugglers. Many of the Atreides are wounded. A soldier called Mattai requests that Gurney sing him a song "to ease his passing".
p320, Dr. Liet Kynes, the Imperial Planetologist.
Having been captured by the Sardaukar, (p262) Liet is given to the Harkonnens who strip him of his stilsuit and send him into the desert to die. He dies in a spiceblow appropriately enough.
p352, Jamis.
Foolishly challenges Paul to a knife fight by insisting that Jessica is a witch and must be championed. He dies.
p387, Undrugged Atreides Slave.
Feyd-Rautha and Thufir Hawat devise a plan to get Feyd adored by the populace of Geidi Prime. The plan is that a captured Atreides soldier be allowed to fight Feyd in the arena without first being drugged to slow him down. As the poison from Feyd blade takes hold the soldier falls on his blade. This is the last suicide in the book (unless you count challenging Paul to a fight).
p412, Reverend Mother Ramallo.
The old and dying Fremen Reverend Mother Ramallo gives up her life to Jessica as Jessica (and Alia) endures the spice agony to become Reverend Mothers themselves.
The Prophet
p423, Slave Boy.
Feyd-Rautha and Thufir Hawat plot to kill the Baron Harkonnen with a slave boy with a poisoned needle in his thigh. The Baron kills the slave boy having been warned by Hawat.
p424, Slave Master.
He is killed by Feyd for being inept at pyramid chess. Feyd is also ordered to kill the two lackeys that cleared up the slave boy (p423).
p429, All the women in the slave quarters.
Feyd is ordered to do this as the price of his life because of the above slave boy incedent.
p474, Several Smugglers.
Paul, who is by now Muad'dib, raids a smuggler spice harvester. This harvesting crew is lead by Gurney Halleck.
p438, Seven Sardaukar and two Fremen.
The Sardaukar were in the above smuggler band. They attack to try and kill Paul. They fail. This is when Paul gets proof of Sardaukar involvement in the form of a knife thrown at his head. The knife has the Imperial Crest on it.
p485, One Sardaukar.
Killed by another Sardaukar, Captain Aramsham for trying to kill Paul when brought before him.
p530, Paul's first son and a number of Fremen and Sardaukar.
Alia allows herself to be captured and tells the Emperor that Paul's first son was killed by the Sardaukar who were only able to escape the Fremen raid by turning the flames from their aircraft's engines on them.
p533, Baron Harkonnen.
Killed by Alia with a poisoned needle: an Atreides Gom Jabbar.
p534, Many, many, Sardaukar and Fremen.
The main attack by the Fremen on Arrakeen.
p540, Rabban "the beast" Harkonnen.
Mentioned by Stilgar in passing to Paul after the attack before they bring the Emperor before them.
p546, Thufir Hawat, Master of Assassins.
Thufir Hawat has been working for the Harkonnens and has been given a poison that requires daily doses of antidote to keep him alive. The Harkonnens withdraw the antidote. He dies valiantly, refusing to kill Paul and save his own life.
p559, Na-Baron Feyd-Rautha Harkonnen.
Foolishly challenges Paul to a knife fight under the rules of Kanly because Duke Leto declared Vendetta on the Harkonnens. Despite his best efforts, a poisoned blade and needle he is eventually killed by Paul by having his brain skewered on Paul's crysknife.
Total Confirmed Kills:
10 Leading characters.
8 Incidental but named characters.
359 Harkonnen sympathisers.
1 unnamed Atreides.
5 unnamed Harkonnens.
7 unnamed Fremen.
416 unnamed Sardaukar.
And a slave boy.
Dune Messiah
p46, Farok and his Son.
Farok, an old Fedaykin, plots against Paul Atreides and invites a face dancer, Scytale, into his house. Scytale kills him and his blind son with poison dart gun.
p92, 61 Billion People.
Reported killed in Paul's Jihad. Ninety-one planets sterilised. Paul tells Stilgar this in passing when telling him about Genghis Kahn and Hitler.
p94, Some Sardaukar.
Some people trample one of the Imperial gardens. Among them are some Sardaukar who Chani picks out. They are executed.
p96, Lichna of Berk al Dib
Paul's people find the body of a Fremen girl addicted to semuta. They don't know it yet but it is Otheym's daughter who was abducted from Farok's house by Scytale.
p161, Otheym and his wife, Dhuri.
Scytale the face dancer gets Paul to visit Otheym the Fedaykin and his wife to pick up a message in the form of the dwarf Bijaz. Moments after Paul leaves a stone burner, atomic weapon, is set off and vapourises them.
p162, Otheym's Neighbours.
Moments later their neighbours are also vapourised. Many people, including Paul, lose their eyes due to the j-rays.
p205, Chani.
Dies in childbirth due to the contraceptive Irulan, Paul's 'wife', was administering to her as part of the plot involving Scytale. She gives bith to Leto II and Ghanima before she dies.
p212, Scytale.
Scytale gets into the nursery with Leto II and Ghanima and threatens to kill. The now blind Paul sees through his son Leto's eyes and manages to throw his crysknife into Scytale's head.
p221, Paul Atreides.
In accordance with Fremen law the truly blind must walk into the desert to die. Paul does this and perishes in the dunes of Arrakis (or does he?).
Total Confirmed Kills:
1 Leading character.
5 Incidental but named characters.
61 Billion unnamed, unaligned characters.
And a god.