Nora Allen - Stabbed by Eobard. Her death was temporarily undone when Barry created Flashpoint, stopping Eobard from killing her.
Fred Chyre - Shot in the neck by Clyde mardon
Clyde Mardon - Shot by Joe.
Fastest Man Alive
Java - Beaten to death by Black and his clones.
Danton Black/Multiplex - Fell out of a window to commit suicide, though the Flash tried to save him.
Simon Stagg - Stabbed by Eobard, disguised as Wells.
Things You Can't Outrun
Araz Darbinyan - Suffocated after inhaling the Mist.
Raffi Darbinyan - Suffocated after inhaling the Mist.
Theresa Howard - Suffocated after inhaling the Mist.
Going Rogue
Basil Nurblin - Shot by Snart.
Plastique
Bette Sans Souci - Shot by Eiling. Her body then became a bomb that nearly destroyed Central City.
Power Outage
Tony Woodward/Girder - Electrocuted by Blackout. Later resurrected as a zombie.
Farooq Gibran/Blackout - Overloaded himself when he tried to steal Barry's speed.
Out of Time
Cisco Ramon - Stabbed by Eobard with his vibrating hand. However, this was in an alternate timeline that Barry prevented.
Rogue Time
Vincent Santini - Shot by Snart.
Mason Bridges - Stabbed by Eobard.
Tricksters
Tess Morgan - Killed in a car crash caused by Eobard.
Harrison Wells - Appearance stolen by Eobard, causing him to decompose.
All Star Team Up
Bill Carlisle - Killed by Larvan's bees.
Lindsay Kang - Killed by Larvan's bees.
The Trap
Hannibal Bates/Everyman - Shot by Joe, thinking he was Wells.
Rogue Air
Jake Simmons/Deathbolt - Shot in the face by Snart.
Fast Enough
Eddie Thawne - Shot himself in order to kill Eobard.
Eobard Thawne/Reverse-Flash - Erased from history after Eddie, his ancestor, killed himself. A time remnant of him was preserved through the Speed Force, allowing him to live.
Season 2
The Man Who Saved Central City
Ronnie Raymond/Firestorm - Killed when he and Martin destroyed the Singularity.
Al Rothstein - Killed by Atom-Smasher, his Earth-2 counterpart.
Al Rothstein/Atom-Smasher - Trapped in a nuclear core by Barry, then absorbed too much energy and overloaded.
Flash of Two Worlds
Eddie Slick/Sand Demon - Turned to glass by Barry, then shattered.
Family of Rogues
David Rutenberg - Killed by Lewis Snart with a bomb in his head.
Lewis Snart - Shot by his son Leonard.
The Darkness and the Light
Eric Larkin - Shot by Doctor Light.
Potential Energy
Russell Glosson/Turtle - Had his brain tissue removed by Wells.
The Reverse-Flash Returns
Francine West - Died of MacGregor's Syndrome.
Welcome to Earth-2
Joseph West - Fatally injured by Deathstorm while trying to save Iris.
Ronnie Raymond/Deathstorm - Stabbed in the back by Zoom.
Francisco Ramon/Reverb - Stabbed in the chest by Zoom.
King Shark
Shay Lamden - Killed in the Particle Accelerator explosion.
Trajectory
Eliza Harmon/Trajectory - Body destroyed by the Speed Force after injecting herself with Velocity-9.
Versus Zoom
Ashley Zolomon - Shot by her husband James.
Back to Normal
Griffin Grey - Died of old Age while fighting the Flash.
Caitlin Snow/Killer Frost - Stabbed by Zoom with her icicle.
Rupture
Dante Ramon/Rupture - Stabbed by Zoom.
The Race of His Life
Henry Allen - Stabbed by Zoom. His death was temporarily undone when Barry created Flashpoint.
Hunter Zolomon/Zoom - Captured by the Time Wraiths and shriveled up. However, the Speed Force turned him into Black Flash to hunt down speedsters who mess with time.
Season 3
Flashpoint
Edward Clariss/Rival - Shot in the back by Joe. This was Undone when Barry destroyed Flashpoint.
Paradox
Dante Ramon - Died in a car crash as one of the post-Flashpoint side effects.
Edward Clariss/Rival - Stabbed by Savitar.
The Present
Iris West - Stabbed through the heart by Savitar. This was prevented when H.R. switched places with Iris, sacrificing himself and ultimately leading to Savitar's destruction.
Untouchable
Stuart Holzman - Touched by Yorkin, causing him to decompose.
Julio Mendez - Touched by Yorkin, causing him to decompose.
Duet
Digsy Foss - Shot by Moran's men.
Cutter Moran - Shot by Foss's men.
Abra Kadabra
Abra Kadabra - Presumably executed by the Collectors.
Finish Line
H.R. Wells - Stabbed in the heart by Savitar, thinking he was Iris.
Hunter Zolomon/Black Flash - Frozen then shattered by Killer Frost
Barry Allen/Savitar - Shot by Iris, then erased from existence by the paradox caused by him failing to kill her.
Season 4
Mixed Signals
Kurt Weaver - Obliterated inside of an elevator being dropped and violently shaken by Ramsey Deacon's technopathy.
Don't Run
Clifford DeVoe - Original Body - Killed after transferring his consciousness and powers into the body of Dominic Lanse.
True Colors
Warden Wolfe - Killed by Clifford Devoe (in the body of Becky Sharpe) when he uses his power-absorbing wheelchair.