New Jedi Order Era

Boba Fett: A Practical Man (e-book), scenes 6-12
The New Jedi Order: Vector Prime (book)
Invasion: Refugees #0-5 (comic)
Boba Fett: A Practical Man (e-book), scenes 13-14
Note: The flashbacks in Chewbacca have been separated into their own places in the timeline, but the series should be read as a whole, as the flashbacks are stories being told
Chewbacca #1-4 (comic)
The New Jedi Order: Dark Tide: Onslaught (book)
The New Jedi Order: Dark Tide: Ruin (book) Ch 1-34
Legacy of the Force: Invincible (book), A Long Time Ago… (flashback between Ch 19/20)
The New Jedi Order: Dark Tide: Ruin (book) Ch 35-End
Boba Fett: A Practical Man (e-book), scenes 15 – End
The New Jedi Order: Agents of Chaos: Hero's Trial (book)
The New Jedi Order: Agents of Chaos: Jedi Eclipse (book)

The New Jedi Order: Balance Point (book)
The New Jedi Order: Edge of Victory: Conquest (book) Prologue
The New Jedi Order: Recovery (e-book)
The New Jedi Order: Edge of Victory: Conquest (book) Ch 1 – End
Emissary of the Void: Battle on Bonadan (short story)
Emissary of the Void II: Dark Tidings (short story)
Emissary of the Void III: The War on Wayland (short story)
Emissary of the Void IV: Relic of Ruin (short story)
The New Jedi Order: Edge of Victory: Rebirth (omnibus), Prologue – Ch 30
Emissary of the Void V: A Perilous Plan (short story)
Emissary of the Void: Episode VI (short story), scenes 1-5
The New Jedi Order: Edge of Victory: Rebirth (omnibus), Ch 31-36
Emissary of the Void: Episode VI (short story), scenes 6-7
The New Jedi Order: Edge of Victory: Rebirth (omnibus), Ch 37-40
Emissary of the Void: Episode VI (short story), scene 8
The New Jedi Order: Edge of Victory: Rebirth (omnibus), Ch 40 – End
Emissary of the Void: Episode VI (short story), scenes 9-14 (end of story)

The New Jedi Order: Star by Star (book)
Note: Parts of Dark Journey, Enemy Lines & Traitor overlap, but I this seems to be the best way of reading them, since they all occur in logical succession.
The New Jedi Order: Dark Journey (book) Ch 1-21, scene 1
The New Jedi Order: The Apprentice (short story), scene 1
The New Jedi Order: Dark Journey (book) Ch 21, scene 2
The New Jedi Order: The Apprentice (short story), scene 2
The New Jedi Order: The Apprentice (short story), scene 3 – End
The New Jedi Order: Dark Journey (book) Ch 21, scene 3 – End
The New Jedi Order: Enemy Lines: Rebel Dream (book)
The New Jedi Order: Enemy Lines: Rebel Stand (book)
The New Jedi Order: Traitor (book)

The New Jedi Order: Destiny's Way (book) Ch 1-21
The New Jedi Order: Ylesia (e-book)
The New Jedi Order: Force Heretic I: Remnant (book) Prologue
The New Jedi Order: Destiny's Way (book) Ch 22 – End
The New Jedi Order: Force Heretic I: Remnant (book) Ch 1 – End
The New Jedi Order: Force Heretic II: Refugee (book)
Or Die Trying (short story)
The New Jedi Order: Force Heretic III: Reunion (book)
The New Jedi Order: The Final Prophecy (book)

X-Wing: Mercy Kill (book) Ch 17
The New Jedi Order: The Unifying Force (book)

Dark Nest I: The Joiner King (book)

Dark Nest II: The Unseen Queen (book)
Dark Nest III: The Swarm War (book)

Fate of the Jedi: Imprint (short story)

Legacy of the Force: Bloodlines (book), Prologue