Previous maps:
Uncanny X-Men #94-280
X-Men 1991-1994
X-Men 1995-2000
2001-2008

Messiah Complex
Messiah Complex #1
UXM #492
X-Factor #25
New X-Men #44
X-Men #205
UXM #493
X-Factor #26
New X-Men #45
X-Men #206
UXM #494
X-Factor #27
New X-Men #46
X-Men #207

Divided We Stand (TPB)
DWS #1-2

Uncanny X-Men:  Divided We Stand (TPB)
UXM #495-499

X-Force:  Legacy of Vengeance
X-Force #1-11

Ghost Boxes (TPB/HC)
AXM #25-30
Ghosts Boxes #1-2

UXM:  Manifest Destiny (HC)
X-Men:  FCBD
UXM #500-503
selected stories from Manifest Destiny #1-5

X-Men Legacy:  Divided He Stands
X-Men:  Legacy #208-216
Wolverine:  Origins #28
Original Sin #1
X:L #217
W:O #29
X:L #218
W:O #30
X:L #219-225

X-Men:  Manifest Destiny (HC)
selected stories from Manifest Destiny #1-5
Wolverine: MD #1-4
MD:  Nightcrawler

Lovelorn (TPB)
UXM #504-507
UXM Annual #2

(Technically, Annual #2 goes between #505 and 506, but putting it at the end doesn’t screw up the story too much.)

Cable:  Messiah Warrior
Cable #1-6
King Sized Cable
Cable #7-12

Messiah War
X-Force #12-13
Messiah War #1
Cable #13
X-Force #14
Cable #14
X-Force #15
Cable #15
X-Force #16
X-Force #17-20
The Life and Times of Lucas Bishop #1-3
Messiah War:  Future History Sourcebook

(Future History is optional.  I included it because it was in the trade.)

Sisterhood (TPB)
UXM #508-512

Dark Avengers/X-Men:  Utopia (HC)
Utopia
UXM #513
Dark Avengers #7
UXM #514
DA #8
Exodus
XM:L #226-227
Dark X-Men:  Beginning #1-3
Dark X-Men:  The Confession

(That’s not the exact order, but as noted, I got the official hardcover.  Also, New Mutants #1-5 and Astonishing X-Men #31-35 probably go somewhere in the midst of this.  But I’m planning on getting those in trades.)

Nation X
X-Men: Legacy Annual #1
X-Men: Legacy #228-230
UXM #515-517
Nation X #1 (all stories)
Nation X #3 (first story)
Necrosha:  The Gathering #1
Necrosha X #1
X-Force #21
New Mutants #6-8
X-Force #22-23
X-Men: Legacy #231-233
X-Force #24-25
Nation X #3 (third story)
UXM #518-519
Nation X #2 (first two stories)
New Mutants #9-10
Nation X #3 (second story)
Nation X #4 (second story)
X-Men Legacy #234
UXM #520-522
Nation X #4 (first, third and fourth stories)
Nation X #2 (third and fourth stories)
Nation X #3 (fourth story)

(I had to combine Nation X and Necrosha X, because Necrosha took place in between Nation X issues.  Also, the Emplate arc from X-Men Legacy can stand on its own.  I included it here because the copy of the TPB I got from Amazon was slightly messed up.  Also, the Nation X limited series can probably be placed in various places.  The first story of #1 has to take place between UXM #517-518, though.  More than likely, when I finally get this bound, those Nation X anthology stories will move around.)

Cable:  Homecoming
Cable #16-20
X-Men:  Hope
Cable #21-25

Second Coming
Second Coming:  Prepare (prelude story only)
Second Coming #1
UXM #523
New Mutants #12
Legacy #235
X-Force #26
UXM #524
NM #13
Legacy #236
X-Force #27
UXM #525
NM #14
Legacy #237
X-Force #28
Second Coming #2

(For the extra features in Second Coming:  Prepare, I will most likely include the cover previews at the back of Second Coming.  The Phoenix Force feature will go either at the end of Nation X or Homecoming.)

At this point, I seriously cut back on my X-Men collecting, so the next few volumes aren’t completely comprehensive.  For one thing, I dropped X-Men Legacy.

The Heroic Age
Uncanny X-Men:  The Heroic Age #1
UXM #526-534
Generation Hope #1-5
Deadpool and Cable #26

(I left the backup story for UXM #526 in place.)

Escape from the Negative Zone (HC)
UXM Annual #3
Super Soldier Annual #1
Namor Annual #1

Dark Angel Saga
Uncanny X-Force #1-4, 5.1, 5-18

Hope and Fear
UXM #534.1
Generation Hope #6-9
UXM #535-543

Schism
Schism #1-3
Generation Hope #10-11
Schism #4-5
X-Men: Regenesis #1
Generation Hope #12
Uncanny X-Men #544

(Some of the Generation Hope issues could be spliced around Schism and Regenesis issues, but they also work unspliced, in a sort of flashback or replay capacity.  Although, if GH #12 didn’t share pages with the Regenesis excerpt, I would likely splice that issue.)

During this era, the focus has shifted more to actual TPBs, so this is almost more of a reading list more than binding map.  When I was deciding to bind, I discovered that it was actually more cost effective to buy the official versions.  Also during this time, writing got more arc-centric and each series started developing its own tone to the point that mixing them together in big volumes just didn’t work out as well.  Plus, there are several spans of time where Marvel went completely overboard with ads, without at least giving us the courtesy of putting them back to back for easy removal.  The official Marvel releases are marked with (TPB) or (HC).  Most X-Treme X-Men books in this list aren’t TPBs, though, because Marvel did a bad job of keeping that series in the proper order, especially with the side projects (minis and one-shots).

This list does contain complete maps for X-Treme X-Men, Morrison’s New X-Men and Excalibur (volume 2).  It also includes the complete Austen run, and Claremont’s third run.

Some of the books could probably slide around.

Destiny Quest
X-Treme X-Men #1-4
Savage Land #1-4

(I originally wanted to separate both of these stories, and put Savage Land after New X-Men started, due to Beast and his physical appearance.  But then I decided it wasn’ t worth the hassle.  Marvel put XXM #1-9 together in one trade, which doesn’t work, because the Savage Land mini has to go between 4 and 5.)

E is For Extinction (TPB)
New X-Men #114-117
New X-Men Annual 2001

Poptopia (TPB)
UXM #394-399

The Godfather
XXM #5-9
XXM Annual 2001

(I got the XXM:  Prisoner of Fire trade which reprinted the 2001 annual, ripped it apart, put the annual here in its proper place, and rebound the rest of the trade.)

Rocktopia
UXM Annual 2001
UXM #400-409

(The problem with the 2001 annuals is that they were done in the sideways “Marvelscope” format.  Nifty idea, but bad for binding.  The UXM annual was the only one not reprinted, so here we have to suffer with rotating the book throughout the issue.  Since the artists never took advantage of using double paged spreads in this format, you don’t have to worry about splicing pictures in half. Of course, Marvel reprints the entire Casey run, including the annual, in one big TPB after I go to the trouble of binding it.)

Imperial (TPB)
New X-Men #118-126

Invasion
XXM #10-18

Hope (TPB)
UXM #410-415

New Worlds (TPB)
New X-Men #127-133

Dominant Species
UXM #416-420

(For some reason, the trade of this is ridiculously high priced now.  So, I’m going to have to bind these.)

Schism
XXM #19
XXM: X-Pose #1-2
XXM #20-24

Holy War (TPB)
UXM #421-427

Mekanix
#1-6

(Another trade that’s hard to find.  In fact, the mini itself is hard to find.)

Riot at Xavier’s
New X-Men #134-141

(At this point, I go away from Marvel’s trades.  #139-141 continue from Riot, while #142-156 sort of keep up a continuous narrative.)

God Loves, Man Kills II (TPB)
XXM #25-30

The Draco
UXM #428-436

(Not the trade, because the Juggernaut 2-parter needed a place to go, in it’s proper place.)

Intifada
XXM #31-39

(I’d actually recommend the two trades for this one.  After binding, I realized that 90% of the right hand pages were all ads.)

She Lies With Angels (TPB)
UXM #437-441

Planet X
New X-Men #142-156

(A lot of people probably don’t like putting two Austen issues here, but not only do they continue directly from the end of Morrison’s last issue, but where else can I put them?)

Prisoner of Fire
XXM #40-46

(As noted above, I actually took the trade apart and rebound with just these issues.)

Excalibur:  Forging the Sword
UXM #442-443
Excalibur #1-7

Astonishing X-Men Volume 1 (HC)
Astonishing X-Men #1-12

Day of the Atom
X-Men #157-164

(The trade includes #165, which I prefered to have later on in the chronology.)

The End of History (TPB)
UXM #444-449

Excalibur:  The Devil’s Own
Excalibur #8-14

The Cruelest Cut
UXM #450-454
X-Men #165

Golgotha (TPB)
X-Men #166-170

Phoenix Endsong (TPB)
#1-5

On Ice (TPB)
UXM #455-461

Wild at Heart
X-Men #171-175
Black Panther #8
X-Men #176
Black Panther #9

(I was trying to get the two trades for this, but one of them is hard to find.  Unfortunately, these issues have a lot of ads.)

—House of M goes here—

House of M:  Uncanny X-Men (TPB)
UXM #462-465

(I’m not including this arc in the actual House of M event, because it ties in very loosely and would disrupt the flow of that book.)

Decimation (TPB)
House of M:  The Day After
X-Men #177-181

Deadly Genesis (HC)
#1-6

End of Greys (TPB)
UXM #466-471

Blood of Apocalypse
Apocalypse vs. Dracula #1-4
Cable and Deadpool #26-27
X-Men #182-187

The First Foursaken (TPB)
UXM #472-474
UXM Annual #1 (why did they start over with #1?)

Supernovas (TPB)
X-Men #188-193
X-Men Annual #1 (the second Annual #1)
X-Men #194-199

Rise and Fall of Shi’Ar Empire (HC)
UXM #475-486

Phoenix Warsong (TPB)
#1-5

Endangered Species (TPB)
X-Men:  Endangered Species #1
back up stories from X-Men #200-204, UXM #488-491, X-Factor #21-24, and New X-Men #40-42

Blinded by the Light (TPB)
X-Men #200-204

The Extremists (TPB)
UXM #487-491

Astonishing X-Men Volume 2 (HC)
AXM #13-24
Giant Size AXM #1

Emperor Vulcan (TPB)
Emperor Vulcan #1-5

Continues:  http://comicbinding.com/mapping/x-men-–-the-messiah-era