Key

HBM – How to Break Into Comics the Marvel Way
MASG - Mystic Arcana: Sister Grimm
RW1 - Runaways (1st series)
RW2 - Runaways (2nd series)
RW3 - Runaways (3rd series)
RYA - Runaways/Young Avengers
RWS - Runaways Saga
STR – Strange (Dr. Strange series)

616 Universe

Runaways - 

Alex Wilder - RW2 #14 (FB), RW1 #17 (FB), 1 - 18, RW2 #24

Chase Stein - RW1 #17 (FB), 1 - 18, RW2 #1, 2, RW2 #19 (FB), 3 - 12, XMR, RW2 #14 - 21, YAR #1 - 4, RW2 #22 - 24, RS1, RW2 #25 - 28, 30, RYA #1 - 3, RW3 #1 - 6,  HBM #1 (FB), HBM #1, RW3 #7 - 9, 10/1, 10/2, 11 - 14

Gertrude Yorkes - RW1 #17 (FB), RW2 #27 (FB as hologram), 1 - 18, RW2 #1, 2 RW2 #19 (FB), 3 - 12, XMR, RW2 #14 - 18

Karla Prast - RW2 #27 - 30, RYA #1 - 3, RW3 #1 - 6,  HBM #1, RW3 #7 - 9, 10/1, 10/2, 11 - 14

Karolina Dean - RW1 #17 (FB), 1 - 18, RW2 #1, 2, RW2 #19 (FB), 3 - 8, RW2 #14, 18 - 21, YAR #1 - 4, RW2 #22 - 24, RS1, RW2 #25 - 30, RYA #1 - 3, RW3 #1 - 6,  HBM #1, RW3 #7 - 9, 10/1, 10/2, 11 - 14. SWD #2 - 3, 5

Molly Hayes - RW1 #17 (FB), 1 - 2, 4 - 18, RW2 #1, 2, RW2 #19 (FB), 3 - 12, XMR, RW2 #13 - 21, YAR #1 - 4, RW2 #22 - 24, RS1, RW2 #25 - 30, RYA #1 - 3, RW3 #1 - 6,  HBM #1 (FB), HBM #1, RW3 #7 - 9, 10/1, 11 - 14, UXH #1

Nico Minoru - RW1 #17 (FB), 1 - 17, RW1 #18 (pg 1 - 3), MASG, RW1 #18 (pg 4 - 23, RW2 #1, 2, RW2 #19 (FB), 3 - 12, XMR, #14 - 21, YAR #1 - 4, RW2 #22 - 24, RS1, RW2 #25 - 30, RYA #1 - 3, RW3 #1 - 6,  HBM #1 (FB), HBM #1, RW3 #7 - 9, 10/1, 10/2, 11 - 14, STR #4

Old Lace - RW1 #2 - 18, RW2 #1, 2, RW2 #19 (FB), 3 - 12, XMR, #14 - 21, YAR #1 - 4, RW2 #22 - 24, RS1, RW2 #25 - 27, 30, RYA #2, 3, RW3 #1 - 6, 8,  10/2, 11, 12

Victor Mancha - RW2 6 (FB), 1 - 12, XMR, RW2 #14 - 21, YAR #1 - 4, RW2 #22 -24, RS1, RW2 #25 - 30, RYA #1 - 3, RW3 #1 - 6,  HBM #1, RW3 #7 - 9, 10/1, 10/2, 11 - 14

Victorious (Victor Mancha alternate future version) - RW2 #2 (FB)

Xavin - RYA #1 (FB), RYA #2 (FB), RW2 #7, 8, RW2 #14, 17 - 21, YAR #1 - 4, RW2 #22 - 24, RS1, RW2 #25 - 30, RYA #1 - 3, RW3 #1 - 6

Avengers -

Luke Cage - RW2 #9, 12

Captain America - RW1 #17, 18, RW2 #9 - 12, YAR #1

Captain America (alternate future version) - RW2 #1 (FB), RW2 #1, 2

Hawkeye - RW2 #6 (FB)

Heroine (Gertrude Yorkes alternate future version) - RW2 #1 (FB), RW2 #1, 2

Hisako (alternate future version) - RW2 #2 (FB)

Iron Man - RW2 #6 (FB), RW2 #10 - 12, 24

Dr. Henry Pym - RW2 #6 (FB)

Scarlet Witch - RW1 #18

Scorpion (alternate future version) - RW2 #1 (FB), RW2 #1, 2

She-Hulk - RW2 #10

Spider-Man - RW2 #10, 11

Spider-Woman I - RW2 #9, 12

Vision - RW1 #18

Wolverine - RW2 #10 - 12, XMR, RW3 #10/1 (as an X-Man)

Wonder Man - RW2 #6 (FB), YAR #1

Avengers Initiative -

Annex - RYA #1

Batwing - RYA #1

Crusader - RYA #1

Gauntlet - RYA #1

Melee - RYA #1

Prodigy - RYA #1

Red Nine - RYA #1

Sunstreak - RYA #1

Excelsior - 

Darkhawk - RW2 #1 - 6

Green Goblin/Phil Urich - RW2 #1 - 6

Lightspeed - RW2 #1 - 6

Ricochet - RW2 #1 - 6

Turbo - RW2 #1 - 6

The Pride -

Frank Dean - RW1 #13 (FB), 17 (FB), 1, 2, 7, 11, 12, 15 - 17

Leslie Dean - RW1 #13 (FB), 17 (FB), 1, 2, 5 - 7, 9, 11, 15 - 17

Alice Hayes - RW1 #13 (FB), RW3 #10/1 (FB), RW1 #17 (FB), 1, 2, 4 - 7, 8 (on screen), 10 - 12, 14 - 17

Gene Hayes - RW1 #13 (FB), RW3 #10/1 (FB), RW1 #17 (FB), 1, 2, 4 - 7, 8 (on screen), 11, 12, 14 - 17

Robert Minoru - RW1 #13 (FB), 17 (FB), 1, 2, 4, 6 - 9, 10, 11, 15 - 17

Tina Minoru - RW1 #13 (FB), 17 (FB), 1, 2, 4, 6 - 9, 11, 15 - 17

Janet Stein - RW1 #13 (FB), RW3 #13 (FB), 1, 2, 4 - 7, 11, 15 - 17

Victor Stein - RW1 #13 (FB), RW3 #13 (FB), RW2 #27 (FB as hologram), RW1 #1, 2, 4 - 9, 11, 12, 14 - 17

Catherine Wilder - RW1 #13 (FB), RW2 #14 (FB), RW1 #17 (FB), 17 (FB), 1 - 4, 6 - 9, 11, 15 - 17

Geoffrey Wilder - RW1 #13 (FB), RW2 #14 (FB), RW1 #17 (FB), 1 - 4, 6 - 9, 11, 14 - 17

Dale Yorkes - RW1 #13 (FB), RW2 #27 (FB as hologram), RW2 #27, 28, 30 (1907), 1, 2, 3 (as hologram), 4 - 7, 10, 11, 15 - 17

Stacey Yorkes - RW1 #13 (FB), RW2 #27 (FB as hologram), RW2 #27, 28, 30 (1907), 1, 2, 3 (as hologram), 4 - 7, 8 (on screen), 11, 15 - 17

The New Pride -

Hunter - RW2 #14 (FB), RW2 #6, 12, 15 - 18

Lotus - RW2 #14 (FB), RW2 #6, 12, 15 - 21

Oscar - RW2 - #14 (FB)

Stretch - RW2 #14 (FB), RW2 #6, 12, 15 - 18

Geoffrey Wilder (younger version) - RW2 #18 (FB), RW2 #14 (FB), RW2 #1 - 6, 12, 15 - 18

School of the Seven Bells -

Bob - RW2 #13

Gordon - RW2 #13

Luis Hernandez - RW2 #13

Maria Hernandez - RW2 #13

Provost - RW2 #13

Suzy - RW2 #13

The Wrecking Crew -

Bulldozer - RW2 #1

Excavator - RW2 #1

Piledriver - RW2 #1

Thunderball - RW2 #1

Wrecker - RW2 #1

X-Men -

Beast - XMR, RW3 #10/1

Colossus - XMR, RW3 #10/1

Cyclops - XMR, RW3 #10/1

Emma Frost - XMR, RW3 #10/1

Lockheed - XMR

Pixie - RW3 #10/1

Shadowcat - XMR

Storm - RW3 #10/1 (as a hologram)

Young Avengers -

Hawkeye - YAR #1 - 4, RYA #1, 2 (on television)

Hulkling - YAR #1 - 4, RYA #1 - 3

Patriot - YAR #1 - 4, RYA #1, 2 (on telelvision)

Speed - YAR #1 - 4, RYA #1 - 3

Stature - YAR #1 - 4, RYA #1 (as Initiative)

Vision - YAR #1 - 4, RYA #1, 2 (on television)

Wiccan - YAR #1 – 4, RYA #1 - 3

Young X-Men -

Anole - RW3 #10/1

Dust - RW3 #10/1

Hellion - RW3 #10/1

Loa - RW3 #10/1

Match - RW3 #10/1

Mercury - RW3 #10/1

Rockslide - RW3 #10/1

Stepford Cuckoos - RW3 #10/1

Surge - RW3 #10/1

Other Characters -

The Adjudicator - RW2 #27 - 30

Ashley - MASG

Chester Biloxi - RW1 #18, RW2 #21

Black Maria - RW2 #28 - 30

Bo - RW2 #10, 11

Bob (KZIT) - RW3 #1, 2

Chrell - RYA #1 (FB), RYA #2, 3 (FB), RYA #1 - 3

Cloak - RW1 #11, 12, RW2 #9 - 12

Creeper - RW2 #27, 29

Cube Warden - YAR #2 - 4

Dagger - RW1 #11, 12, RW2 #10 (FB), RW2 #9 - 12

Daredevil - YAR #1

Daystick - RW2 #28 - 30

Dead George Pelham - RW2 #27, 29, 30

Deering - RW3 #12, 13

Sgt. deHalle (Majasdanian) - RW3 #2 (FB), RW3 #1 - 3, 5, 6

Difference Engine - RW2 #28 - 30

Doombot - RW2 #4, 5

Dr. Nemesis - RW3 #10/1

Douglas (NYPD officer) - RW1 #2, 3

Falcon - YAR #1

Flagsmasher II - YAR1

Lieutenant Flores - RW1 #3, 6, 11 - 14

Forget-Me-Not - RW2 #27, 28

Fremin - RYA #1 (FB)

Gert lookalike - RW3 #14

The Gibborim - RW1 #13 (FB), 17, RW2 #16, 20 - 22, 24

Goldbrick - RW2 #29

Destiny Gonzales - RW1 #1, 2, 6

Eddie Gunman - RW2 #27 - 30

Maria Hill - YAR #2, 4 (on screen)

Megan Hoyden - RW2 #27, 29

Jacob - RW2 #27

Madison Jeffries - RW3 #10/1

Rick Jones - RW2 #2, 5, 6

Jorge - RW2 #1 - 3

Kid Twist - RW2 #27 - 30

Kingpin - RW2 #25, 26, 30

Father Lantom - RW2 #9 - 12

Marie LaVeau - MASG

Cadie McDunnough - RW1 #18, RW2 #21, RW3 #6

Mr. Maneater - RW2 #27 - 30

Marianella Mancha - RW2 #6 (FB), #3 - 5

Reginald Mantz - RW2 #10 (FB), RW2 #9 - 12

Lillie McGurty (younger version) - RW2 #27 - 30

Lillie McGurty (older version) - RW2 #25, 26, 30

Morphine - RW2 #27 - 29

Mother (Monk Theppie) - RW3 #7, 9

Noh-Varr - YAR #3 (FB), YAR #2 - 4

Nightstick - RW2 #28 - 30

Mr. Prast - RW2 #27, 28

Professor Duck - RW2 #29

Punisher - RW2 #25, 26, 30

Pusher Man - RW2 #10, 11

Pusher Man's doorman - RW2 #10

Dr. Kavita Rao - RW3 #10/1

Ratdog - RW2 #29, 30

The Retching Pigs (rock band) - RW3 #7 

Seth - MASG

S.H.I.E.L.D. Agents - RW2 #24

Silver Bullet Gang - RW2 #22

Sons of the Serpent - RW3 #10/2

Hunter Stein - RW3 #13 (FB), RW3 #11 - 14

Lydia Stumpmeyer  (Val Rhymin's secretary) - RW3 #7 - 9

Swarm - RW2 #7

Topher - RW1 - #7 - 10

Topher's victims/parents - RW1 - #7, 8, 10

Tristan (older version) - RW2 #25 - 26, 30

Tristan (younger version) - RW2 #27 - 30

Ultron - RW2 #6 (FB), 5

Unnamed detective - RW2 #19, 21

Unnamed Pride sacrifice (1) - RW1 #13 (FB)

Unnamed Pride sacrifice (2) - RW1 #17 (FB)

vaDanti (Majesdanian) - RW3 #2 (FB), RW3 #1 - 4, 6

vaDrann (Majesdanian General - RW3 #1 - 3, 5, 6

Val Rhymin (KZIT) - RW3 #1 - 3, 6 - 9

vaRikk (Majesdanian) - RW3 #1 - 3, 5, 6

Queen Veranke - RYA #1 (FB)

Violet (Hunter Stein's secretary) - RW3 #11, 12, 14

Walters - RW2 #19, 20

Walton - RW3 #11 - 13

Witchbreaker RW2 #28, 29

X'iv - RYA #1 - 3

Yellow Kid -  RW2 #27, 30

Note: There is a flashback sequence in Runaways (2nd series) #27 featuring a holographic representation of Gertrude, Victor Stein and the Yorkes'. The timeframe is unclear, but I'm presuming that this scene is set shortly before the Rite of Thunder, which Victor calls the 'Tribute,' shown in the first series. That would position it after the flashback sequences told by Alex in Runaways (1st series) #17. If anyone has any other theories, please don't hesitate to contact me.

Alternate versions

Marvel Zombies-verse

Key

MZ - Marvel Zombies vs. The Armies of Darkness

Karolina Dean - MZ #2

Nico Minoru - MZ #2

Chase Stein - MZ #2

Gertrude Yorkes - MZ #2

What If? Universe

The runaways featured in five What If? issues at the end of 2008 as the Young Avengers. These issues took place in a different universe to the normal 616 Marvel Universe.

Key

BiB - What If? Spider-Man: Back in Black #1
FS - What If? Fallen Son #1
HoM - What If? House of M #1
NFF - What If? Newer Fantastic Four #1
SW - What If? Secret Wars #1
FB - Flashback  

The Runaways/Young Avengers

Karolina Dean - HoM (FB), BiB (FB), HoM, NFF, BiB, SW

Molly Hayes - HoM (FB), BiB (FB), HoM, BiB, SW

Nico Minoru - HoM (FB), BiB (FB), HoM, NFF, BiB, SW

Chase Stein - HoM (FB), BiB (FB), HoM, FS, NFF, SW

Gertrude Yorkes - HoM (FB), BiB (FB), HoM, FS, NFF, BiB, SW

Old Lace - HoM (FB), BiB (FB), HoM, FS, SW

Avengers

Captain America - HoM (FB)

Iron Man - HoM (FB)

Vision - HoM (FB)

The Wrecking Crew

Excavator/Shovel Kid - HoM

Piledriver - Hom

Thunderball - HoM

Wrecker - HoM

Other Characters

Iron Lad - HoM (FB), BiB (FB), FS, NFF,BiB

Kang – (HoM (FB), NFF, BiB

Victor Mancha - BiB (FB), HoM, FS, NFF, BiB, SW

Victorious – HoM (FB), BiB (FB), FS, NFF, BiB, SW

Molly featured in a one-shot What If? issue in 2010. This issue took place in a different universe to the normal 616 Marvel Universe. This story is a variation of Astonishing X-Men (3rd series) #6-12 and Runaways (2nd series) #1-6 and unrelated to the earlier What If? issues.

Key

WIAXM - What If? Astonishing X-Men #1

Runaways -

Molly Hayes - WIAXM