I have finally compiled the complete list of all comics featuring Eobard Thawne. I have excluded reprint comics and ones where he is just an image or flashback and not specifically relevant. I hope people find this helpful.

Reverse Flash Comics

The Flash 1963 – 1985

Issue 139 Menace of the reverse flash

Issue 147 Our Enemy the Flash

Issue 153 The Mightiest punch of all time

Issue 165 One bridegroom too many!

Issue 175 Race to the end of the universe

Issue 186 Time times three equals

Issue 225 Green Lantern Master criminal pf the 25th century

Issue 233 The deadly secret of the Flash

Issue 237 The 1000 year separation

Issue 281 Deadly Games

Issue 282 Mishmash

Issue 283 Flashback

Issue 284 Run Flash, Run for your life

Issue 300 A flash odyssey

Issue 321 Hell in the fast lane

Issue 322 Burning a speedster at both ends

Issue 323 Run Flash, Run for your wife

Issue 324 The slayer and the slain

DC Comics Presents:1978

Issue 1 Superman and The Flash: Chase to the end of time!

Issue 2 Superman and The Flash: Race to the end of time!

The Secret Society of Super-Villains 1978

Issue 12 The Plunder Plan

Issue 13 One earth too many

Issue 14 Crisis on Earth 3

Issue 15 The Wizard’s war of the worlds

Justice League of America 1979

Issue 166 The long way home

Issue 167 The league that defeated itself

Issue 168 The last great Switcheroo

The Flash 1993-2008

73-79 is one arc and you need to read all of it.

Issue 73 One perfect gift

Issue 74 Trust

Issue 75 Running behind

Issue 76 Identity crisis

Issue 77 Suicide Run

Issue 78 Blitzkrieg

Issue 79 The once and future Flash

Issue 146 Time like a river

Issue 147 Shooting the Rapids

Issue 148 Undertow

Issue 223 The RF vs the Rogues

Issue 224 reverse time

Issue 225 the final run

DC Universe Halloween Special 09 (its only one panel but it’s so Eobard)

The Flash: Rebirth 2009 (Eobard isn’t in all of these but they are one plot arc)

Issue 1 Lightning strikes twice

Issue 2 Dead Run

Issue 3 Rear view mirrors

Issue 4 Flash Facts

Issue 5 Mother, May I

Issue 6 Fastest man alive

DC Super Friends 2010

Issue 27 Double Trouble

Batman Beyond 2010

Issue 6 Hush Beyond Part 6: Deep Down. There is a Dr Thawne hired as a geneticist at the end of the comic but no implication that it is Eobard and the future is not far enough to be him, but time travel, so yeah, why not. The same Dr Thawne appears in Batman Beyond 2011 issue 8, still working for Cadmus.

The Flash 2010 Blackest Night

Issue 1, 2 & 3

Brightest Day 2010-2011 (Very minor parts)

Issue 0 Carpe Diem

Issue 7 The secret of life

The Flash 2011 – Brightest Day & Road to Flashpoint

Issue 7 What goes around, comes around

Issue 8 Reverse Flash: Rebirth

Issue 10 Case Two: The road to Flashpoint part 2

Issue 11 Case Two: The road to Flashpoint part 3

Issue 12 Case Two: The road to Flashpoint part 4

Flashpoint 2011

Issue 1, 4 & 5 specifically though you should read all of them for context.

Flashpoint: Reverse Flash

Time Masters: Vanishing Point

Issue 5 Reversing time

Issue 6 Start time/ end point

DC Universe Online: Legends

Issue 23 Victory! (It’s only one panel of Eobard trying to feed Barry to Killer Croc)

Flash 2015 N52 (this is all one plot)

Flash Annual 4

Issue 40 The end of the road

Issue 41 Yellow

Issue 42 Blood is thicker

Issue 43 Getting the drop

Issue 44 Bubble

Issue 45 Thunderdrome

Issue 46 End of the Hunt

Issue 47 Reunion

The Flash 2016 – 2020

Issue 7 Lightning strikes twice part 7: No more speedsters (Really minor, 1 panel)

Issue 19 Sins of the father pt 2 (The ending is the start of The Button arc that crosses with Batman)

Batman: Issue 21 The button pt1

Issue 21 The button pt 2

Batman: Issue 22 The button pt3

Issue 22 The button pt4

Issue 23 The color of fear pt 1: Hello

Issue 24 The color of fear pt 2: Run for your life

Issue 25 Running scared pt 1: Every breath you take

Issue 26 Running scared pt 2: One way or another

Issue 27 Running scared conclusion: I will possess your heart

Issue 46 Road to Flash war

Issue 81 Death and the Speedforce (only one flashback panel)

Deathstroke 2018

Issue 25 The Society

DC Nuclear Winter special 2019

The Flash 2016 – 2020 – Continued

Issue 88 Flash Age Prelude: Paradox

Issue 750 Flash Age 1: Extra Size Spectacular (They changed the numbering at this point, going from 88 to 750)

Issue 751 The Flash Age 2 (Eobard isn’t really in this one but it is part of the arc)

Issue 752 The Flash Age 3

Issue 753 The Flash Age 4: Search for Reverse Flash

Issue 754 The Flash Age 5: The last temptation of the Flash

Issue 755 The Flash Age finale

Issue 756 Reverse Flash family

Issue 757 Legion of Zoom pt 1

Issue 758 Legion of Zoom pt2

Issue 759 Finish line pt 1

Issue 760 Finish line pt 2

Issue 761 Finish line pt 3

Issue 762 Finish line pt 4

Tales from the Dark Multiverse

Issue 8 Flashpoint