Archer & Armstrong
Archer & Armstrong #0-12

Harbinger
Harbinger #0-25
Harbinger Files #1

Solar, Man of the Atom
Solar, Man of the Atom #0 (Alpha and Omega TPB)
Solar, Man of the Atom #1-11
Unity #0
Solar, Man of the Atom #12-13
Unity #1

Solar:  Brave New World
Solar, Man of the Atom #46-54

X-O Manowar Volume 1
X-O Manowar #0-12
Solar, Man of the Atom #17
X-O Manowar #13-15

X-O Manowar Volume 2
X-O Manowar #16-24
Armorines #0 (comes bound in X-O #25)
X-O Manowar #25-32
X-O Database #1

The 41st Century

Magnus Robot Fighter (4001 A.D.)
Magnus Robot Fighter #0-20 (#5-8 include the Rai #1-4 flip books)

The flip books are easy enough to separate and flip around, except for Magnus #5/Rai #1.  The final page of each story was printed back to back, so scanning and printing it required.  But at least, you can fix the credit mix-up for Rai #1, using the credits printed on the Jim Shooter page of Magnus #6.  I kept the cover for Rai #4/Magnus #8 together, since it was one large image.

Rai (4001 A.D.)
Rai #1-8

(I just got the Valiant Masters HC for Rai)

The Malev War:  Volume 1 (4002 A.D.)
Rai #0
Magnus Robot Fighter #21-24
Rai and the Future Force #9
Magnus Robot Fighter #25
Rai and the Future Force #10
Magnus Robot Fighter #26
Rai and the Future Force #11
Magnus Robot Fighter #27
Rai and the Future Force #12
Magnus Robot Fighter #28
Rai and the Future Force #13
Magnus Robot Fighter #29
Rai and the Future Force #14

The Malev War:  Volume 2 (4003 A.D.)
Rai and the Future Force #15
Magnus Robot Fighter #30
Rai and the Future Force #16
Magnus Robot Fighter #31
Rai and the Future Force #17
Magnus Robot Fighter #32-33
Rai and the Future Force #18
Magnus Robot Fighter #34
Rai and the Future Force #19
Magnus Robot Fighter #35
Rai and the Future Force #20
Magnus Robot Fighter #36
Rai and the Future Force #21
Magnus Robot Fighter #37
Rai and the Future Force #22

Magnus:  The Terran Consortium (4020 A.D.)
Magnus Robot Fighter #38
Rai and the Future Force #23
Magnus Robot Fighter #39
Rai #24 (May 19, 4020)
Magnus Robot Fighter #40
Rai #25 (April 24, 4020)
Solar Man of the Atom #38
Psi-Lords #3
Rai #26
Magnus Robot Fighter #41
Magnus Robot Fighter #42-46
Rai #27-33
Magnus Robot Fighter #49-54

(Magnus #47-48 was a fill in that did not fit in the timeframe of the issues around them.)

Acclaim Miscellaneous – This one was a collection of stuff that effectively had nowhere else to go. 
Acclaim Comics Valiant Heroes Special
Acclaim Reader (B/W preview)
Concrete Jungle 1 (I thought about adding the Concrete Jungle Retailer Preview but the series was only one issue, so I decided against it)
The Goat H.A.E.D.U.S. (This could have gone in my Quantum & Woody bind, but it felt more like a separate issue than a crossover)
N.I.O. #1-4
Master Darque Special
Darque Passages #1-4
Deadside #1-3 (Issue 4 was never published! So the mini-series is unfinished)
Unity 2000 Alpha 
Unity 2000 Omega
Unity 2000 #1-3 (another unfinished mini-series. Issues 4-6 never published)

Archer & Armstrong
Archer & Armstrong #0-25
Eternal Warrior #25
Archer & Armstrong #26

Armorines
Armorines #0-12
Armorines (volume 2) #1-4

Bloodshot - Book 1
Bloodshot #0-18

Bloodshot - Book 2
Bloodshot #19-27
Secret Weapons #20
Bloodshot #28
Secret Weapons #21
Bloodshot #29-35

Bloodshot - Book 3
Bloodshot #36-51
Bloodshot Yearbook #1
Bloodshot Last Stand #1

Chaos Effect
Chaos Effect Alpha
Shadowman #29
Second Life of Dr Mirage #11
Turok Dinosaur Hunter #16
Secrets of the Valiant Universe #2
Bloodshot #20
Secret Weapons #13
Ninjak #8
Eternal Warrior #26/Archer & Armstrong #26 (flip-book, EW comes first)
Harbinger #34
Armorines #5
X-O Manowar #33
H.A.R.D. Corps #23
Solar Man of the Atom #38
Psi-Lords #3
Rai #26
Magnus Robot Fighter #41
Chaos Effect Omega
Chaos Effect Epilogue #1
Chaos Effect Epilogue #2

Doctor Tomorrow
Doctor Tomorrow #1-12

Eternal Warrior – Book 1
Valiant Era Companion #1 (included with Valiant Era Collection TPB)
Eternal Warrior #1-17
Eternal Warrior Yearbook #1
Eternal Warrior #18-20

Eternal Warrior – Book 2
Eternal Warrior #21-24
Archer & Armstrong #25
Eternal Warrior #25-27
Eternal Warrior Yearbook #2
Eternal Warrior #28-40

Eternal Warrior - Book 3
Eternal Warrior #41-50
Eternal Warrior Special #1
Fist and Steel #1-2
Eternal Warriors #1-6

Geomancer/Psi-Lords
Geomancer #1-8
Psi-Lords #1-7
Destroyer #0
Psi-Lords #8-10

(Each title individually seemed to be a waste to bind separately.)

Harbinger – Book 1
Harbinger #0-25

Harbinger – Book 2
Harbinger #26-41
Harbinger Files #1-2
Harbinger:  Acts of God (Acclaim)

H.A.R.D. Corps - Book 1
HARD Corps #1-16

H.A.R.D. Corps - Book 2
HARD Corps #17-18
Harbinger #30
HARD Corps #19
Harbinger #31
HARD Corps #20-30

H.A.R.D. Corps (Alternate map to include everything)
HARD Corps #1-18
Harbinger #30
HARD Corps #19
Harbinger #31
HARD Corps #20-22
Armorines #4-5
X-O Manowar #33
HARD Corps #23-30

Magnus Robot Fighter - Book 1
Magnus Robot Fighter #0-20

Magnus Robot Fighter - Book 2:  The Malev War
Magnus Robot Fighter #21 – 24
Rai and the Future Force #9
Magnus Robot Fighter #25
Rai and the Future Force #10 – 11
Magnus Robot Fighter #26 – 29
Rai and the Future Force #15
Magnus Robot Fighter #30
Rai and the Future Force #16
Magnus Robot Fighter #31
Rai and the Future Force #17
Magnus Robot Fighter #32 – 33
Rai and the Future Force #18
Magnus Robot Fighter #34
Rai and the Future Force #19
Magnus Robot Fighter #35
Rai and the Future Force #20
Magnus Robot Fighter #36
Rai and the Future Force #21
Magnus Robot Fighter #37
Rai and the Future Force #22 – 23
Magnus Robot Fighter #38

Magnus Robot Fighter - Book 3
Magnus Robot Fighter #39-40
Magnus Yearbook #1
Magnus Robot Fighter #41-42
Chaos Effect Epilogue #1-2
Magnus Robot Fighter #43-64

Magnus Robot Fighter - Book 4 (Crossovers and VH-2)
Magnus/Nexus #1-2
Predator vs Magnus #1-2
Magnus Robot Fighter (volume 2) #1-18

Ninjak - Book 1
Ninjak #0
Ninjak #00
Ninjak #1-10
Ninjak Yearbook #1
Ninjak #11-17

Ninjak - Book 2
Ninjak #18-26
Ninjak (volume 2) #1-12

Quantum and Woody
Quantum and Woody #0-21, 32

Quantum and Woody (alternate map – publishing order)
Quantum and Woody #1-6, 0, 7-17, 32, 18-21

Rai - Book 1
Magnus Robot Fighter #5-8*
Rai #1-8
Rai Companion #1 (included with Rai TPB)
Rai #0
Rai and the Future Force #9
Magnus Robot Figher #25
Rai and the Future Force #10-14

*(these are Magnus/Rai flip books so I sliced them in half and had them bound in order)

Rai - Book 2
Rai and the Future Force #15
Magnus Robot Fighter #30
Rai and the Future Force #16
Magnus Robot Fighter #31
Rai and the Future Force #17-18
Magnus Robot Fighter #34
Rai and the Future Force #19
Magnus Robot Fighter #35
Rai and the Future Force #20
Magnus Robot Fighter #36
Rai and the Future Force #21
Magnus Robot Fighter #37
Rai and the Future Force #22 – 23
Rai #24-33

The Second Life of Doctor Mirage
The Second Life of Doctor Mirage #1-5
Shadowman #23
The Second Life of Doctor Mirage #6-18

Shadowman - Book 1
Shadowman #1-22
Doctor Mirage #5
Shadowman #23

Shadowman - Book 2
Shadowman #24-43
Shadowman #0
Shadowman Yearbook #1

Shadowman - Book 3
Shadowman (volume 2) #1-20
Shadowman (volume 3) #1-6

Solar - Book 1
Solar, Man of the Atom #0 (Alpha and Omega TPB)
Solar, Man of the Atom #1-23

(I used the TPB For #0 as the inserts did not work correctly because at least one page was on a main story page, not contained to the pullout sections)

Solar – Book 2
Solar, Man of the Atom #24-45

Solar – Book 3
Solar, Man of the Atom #46-60
Destroyer #0
Man of the Atom #1 (Acclaim)
Revelations #1
Solar Hell on Earth #1-4

Timewalker
Timewalker #0-15
Timewalker Yearbook #1

Trinity Angels
Trinity Angels #1-12
Trinity Angels Retailer Preview

Troublemakers
Troublemakers #1-19

Turok Dinosaur Hunter – Book 1
Turok Dinosaur Hunter #0-23

Turok Dinosaur Hunter - Book 2
Turok Dinosaur Hunter #24-47

Turok Dinosaur Hunter - Book 3
Turok the Hunted #1-2
Turok/Timewalker #1-2
Turok: The Empty Souls
Turok: Spring Break in the Lost Land
Turok: Redpath
Turok: Child of Blood
Turok: Tales of the Lost Land
Turok #1-4
Turok/Shadowman
Turok 3: Shadow of Oblivion
Turok: Evolution

Unity
Unity #0
Eternal Warrior #1
Archer and Armstrong #1
Magnus Robot Fighter #15
X-O Manowar #7
Shadowman #4
Rai #6
Harbinger #8
Solar, Man of the Atom #12
Eternal Warrior #2
Archer and Armstrong #2
Magnus Robot Fighter #16
X-O Manowar #8
Shadowman #5
Rai #7
Harbinger #9
Solar, Man of the Atom #13
Unity #1

(I didn’t include the Unity Lost Chapter book because it was published two years after Unity and really reads more like a X-O Manowar book, not a Unity book. So it will be going in the X-O books.)

Valiant Miscellany
Valiant Reader
Secrets of the Valiant Universe #1-3
Valiant Era Companion
Darque Passages
Deathmate Preview Green
Deathmate Preview Pink
Deathmate Prologue
Deathmate Black
Deathmate Yellow
Deathmate Blue
Deathmate Red
Deathmate Epilogue
Deathmate Tourbook
Valiant Free View
The Outcast Special
Punx #1-3
Manga Punx Special
Valiant Vision Starter Kit
Wizard – The Beginning of the Valiant Era
Radioactive Man #106

Vintage Valiant
Vintage Magnus #1-4
Original Magnus #1
Original Doctor Solar #1
Original Turok #1-2
Captain Johner and the Aliens #1-2

The Visitor
The Visitor vs the Valiant Universe #1-2
The Visitor #1-13

X-O Manowar – Book 1
X-O Database
X-O Manowar #0-8
Unity: the Lost Chapter
X-O Manowar #9-21

X-O Manowar – Book 2
X-O Manowar #22-41
X-O Manowar Yearbook #1
X-O Manowar #42
Shadowman #37
X-O Manowar #43

X-O Manowar – Book 3
Birthquake Prequel
X-O Manowar #44-49
X-O Manowar #50-X
X-O Manowar #50-O
X-O Manowar #51-68

X-O Manowar – Book 4
X-O Manowar/Iron Man
Iron Man/X-O Manowar
X-O Manowar (volume 2) #1-2
X-O Manowar (volume 2) Fan Edition
X-O Manowar (volume 2) #3-7
Operation Stormbreaker
X-O Manowar (volume 2) #8-21