The following looks at which In the Comics sub-entries have yet to have full Handbook profiles in the 2004-on era. I’ll skip the redundant “Guidebook to the Marvel Cinematic Universe: Marvel’s…” bits. If the In the Comics bit differs from the MCU entry name, the former is noted in parentheses, though do note that In the Comics sub-entries lack any real titles. +=profiled in the original Handbooks; *=profiled in a Files book. @=only modern profile was a sub-entry
 
Iron Man
Arc Reactor (Stark’s armored chest plate, Repulsor-Tech)
Christine Everhart
Iron Man’s Armors+
JARVIS
 
Incredible Hulk/Iron Man 2
Incredible Hulk
All covered
Iron Man 2
Hammer Industries
Iron Man Armors update (Iron Man’s Briefcase+)
Anton Vanko (Borderline case. This one’s tricky because he did have a shared profile in Marvel Legacy: The 1960s Handbook, which is a variation on regular profiles; however, the hardcover profile was for the armours rather than Vanko)
 
Thor
Laufey
Erik Selvig (Dr. Eric Solvang)
 
Captain America: The First Avenger
Captain America’s Costumes & Shields (costumes only)
Senator Brandt (Emil Gruber)
Sergeant Duffy
Yggdrasil
 
Avengers
Chitauri (616 only)
World Security Council (SHIELD executive council)
 
Iron Man 3/Thor: The Dark World
Iron Man 3
Extremis Soldiers (Extremis, Ellen Brandt)
Iron Man Armors+ update
Iron Patriot/James Rhodes/War Machine (Iron Patriot armor)
Aldrich Killian
Thor: The Dark World
All covered
 
Captain America: The Winter Soldier/Ant-Man
Captain America: The Winter Soldier
All covered
Ant-Man
Jim Paxton (Blake Burdick)
Hope Van Dyne (Red Queen)
Mitchell Carson
Maggie Lang (Peggy Rae)
 
Agents of SHIELD Season 1
Leo Fitz
Melinda May
Jemma Simmons
Grant Ward
Lorelei+
Chan Ho Yin (Scorch/Tommy Ng)
 
Guardians of the Galaxy
[Note that while Star-Lord has been “kissed”, the revelation that there are two key comic book Star-Lords (Quill) renders the older entries outdated, as the older entries treated them as the same person]
Knowhere
Yondu Udonta (616 only)
Xandar
Broker
Rhomann Dey
Nova Prime
Meredith Quill (both realities)
 
Avengers: Age of Ultron
FRIDAY (second Friday)
Iron Man Armors+ update
Barton Family (Ultimate version)
 
Agents of SHIELD Season 2/Agent Carter Season 1
Agents of SHIELD Season 2
Alphonso Mackenzie+
Agent 33
Izzy Hartley (Isabelle, surname unknown)
Daniel Whitehall (aka Kraken)
Agent Carter Season 1
Howling Commandos (“Happy” Sam Sawyer+)
Leet Brandis
Roger Dooley
Leviathan*
Red Room
 
Agents of SHIELD Season 3/Agent Carter Season 2
Agents of SHIELD Season 3
Hive
Holden Radcliffe
Elena “Yo-Yo” Rodriguez (Yo-Yo Rodriguez)
Werner von Strucker
Agent Carter Season 2
Council (Council of Nine)
Jason Wilkes
Zero Matter (Darkforce)
 
Captain America: Civil War
The Raft
Miriam (Miriam Sharpe)
Everett K. Ross
T’Chaka
 
Doctor Strange
Cloak of Levitation
Dark Dimension
Eye of Agamotto@
Kaecilius
Kamar-Taj
Magical Relics (Book of Cagliostro@, Crimson Bands of Cyttorak, Valtoor, Wand of Watoomb)
Masters of the Mystic Arts (Daniel Drumm, Hamir, Tina Minoru)
Christine Palmer (as separate character from other Night Nurses)
Sanctums (Doctor Strange's Sanctum Sanctorum+)
Nicodemus West