I assume that makes the X-Men referenced in Spider-Man: The New Animated Series the Fox versions in this head-canon?
Here's an idea for that:
Instead of six months between 1x06 and 1x12-1x13, substitute that for six weeks and assume the officer mispoke. That way, it places the ending of the show in January-February, 2004, at least a month before Spider-Man 2 begins. Then, say Lizard survived and Curt was cured. That, or use the time travel in Days of Future Past to have the Spider-Man trilogy replace TNAS.
I guess include the non-canon video game sequels, The Punisher and Spider-Man: Friend or Foe, just for completion.
Crossovers
Captain America
Namor and the Human Torch are referenced.
Blade
-A Fantastic Four t-shirt appears in Blade: Trinity.
-Moon Knight is referenced in Blade: The Series.
-Blade read an Avengers comic book as a child in Blade: The Series. Thankfully, no Hulk on the cover. The Avengers are either just a comic book in this head-canon or they assembled in the 1960s-1970s, and Peter hasn't heard of them by 2024.
-In a branched timeline, mutants are referenced. Kingpin is turned into a similar vampire to Pearl. There's a team known as the New Avengers, consisting of Kurt Wagner (Nightcrawler), Hobie Brown (the Hornet/Spider-Punk) and Silver Sable.
X-Men/Wolverine/Deadpool/New Mutants
-Franklin Richards is mentioned in X2: X-Men United. We can use this to indicate that they had a child in the original timeline.
-Hydra appears in X2: X-Men United and Deadpool.
-A crashed helicarrier appears in Deadpool.
-In The Gifted, the Struckers are related to Baron Von Strucker. Andrea von Strucker also appeared in Nick Fury: Agent of S.H.I.E.L.D.
Spider-Man
-Peter has a comic book poster of Elektra in Spider-Man.
-Kingpin appears in Spider-Man: The New Animated Series.
-Stark Industries is referenced in Spider-Man: The New Animated Series.
-The X-Men are referenced in Spider-Man: The New Animated Series.
-Doctor Strange is referenced in Spider-Man 2.
-Nick Fury and Blade appear in Spider-Man: Friend or Foe.
-Punisher appears in Spider-Man 2. FAKE
Hulk
-????.
The Punisher
-Iron Man, Nick Fury, Matt Murdock, Black Widow, Bullseye, and Kingpin (white, lol) are in the video game tie-in. The Thing and Captain America are referenced.
Daredevil/Elektra
Stark Industries is referenced in Elektra: On the Rise #1.
Ghost Rider
-Blade appears in the video game tie-in.
Man-Thing
-A child is wearing a Spider-Man t-shirt in Man-Thing vol. 4 #1.
Fantastic Four
-Reed morphs his face into Wolverine in Fantastic Four: Extended Edition.
Timeline
1959 -
X-Men: First Class: The High Hand #1
1962 -
X-Men: First Class
--DoFP Timeline--
1979 -
X-Men Origins: Wolverine
2003 -
X-Men
2003 -
X-Men 2: Wolverine
2003 -
X-Men 2: Nightcrawler
2003 -
X2: X-Men United
2005 -
X-Men: The Official Game
2006 -
X-Men: The Last Stand
2013 -
The Wolverine: Unleashed Extended Edition
2013 - The Bent Bullet: JFK and the Mutant Conspiracy
2016 - Deadpool (Test Footage)
2016 - The Gifted: Thunderbolt
2016 - The Gifted: Polaris
2016 - The Gifted: Eclipse
2016 - PSA: Sentinel Services
2017 -
The Gifted 1x01, "eXposed"
2017 -
The Gifted 1x02, "rX"
2017 -
The Gifted 1x03, "eXodus"
2017 -
The Gifted 1x04, "eXit strategy"
2017 -
The Gifted 1x05, "boXed in"
2017 -
The Gifted 1x06, "got your siX"
2017 -
The Gifted 1x07, "eXtreme measures"
2017 -
The Gifted 1x08, "threat of eXtinction"
2017 -
The Gifted 1x09, "outfoX"
2017 - Empower Academy
2017 -
The Gifted 1x10, "eXploited"
2017 -
The Gifted 1x11, "3 X 1"
2017 - Circle of Truth
2017 -
The Gifted 1x12, "eXtraction"
2017 -
The Gifted 1x13, "X-roads"
2017 - Trask Industries: Your Future
2017 -
The Gifted 2x01, "eMergence"
2017 -
The Gifted 2x02, "unMoored"
2017 -
The Gifted 2x03, "coMplications"
2017 -
The Gifted 2x04, "outMatched"
2017 -
The Gifted 2x05, "afterMath"
2017 -
The Gifted 2x06, "iMprint"
2017 -
The Gifted 2x07, "no Mercy"
2017 -
The Gifted 2x08, "the dreaM"
2017 -
The Gifted 1x09, "gaMe changer"
2017 -
The Gifted 1x10, "eneMy of My eneMy"
2017 -
The Gifted 1x11, "meMento"
2017 -
The Gifted 1x12, "hoMe"
2017 -
The Gifted 1x13, "teMpted"
2017 -
The Gifted 1x14, "calaMity"
2018 -
The Gifted 1x15, "Monsters"
2018 -
The Gifted 1x16, "oMens"
2018 - 25 Moments in the Struggle between X-Men and Humans
2023 - Trask Industries: Your Future
-----------------------
1973 -
X-Men: Days of Future Past: The Rogue Cut
1982 - In the Footsteps of... En Sabah Nur
1983 - Xavier's School for Gifted Youngsters TV Commercial
1983 - X-Men: Apocalypse: Stan Lee Voicemail Message
1983 - Fables of the Flush & Fabulous
1983 -
X-Men: Apocalypse
1983 - X-Men: Apocalypse: Xavier's School for the Gifted Campus Tour
1986 -
Howard the Duck
1986 -
Howard the Duck: Adventure on Volcano Island
1990 -
Captain America: Director's Cut
1992 -
X-Men: Dark Pheonix
1997 -
Nick Fury: Agent of S.H.I.E.L.D.
1998 -
Blade (PlayStation)
1998 -
Blade (Game Boy Color)
1998 -
Blade: Cybercomic #1
1998 -
Blade: Sins of the Father #1
1998 -
Blade
--V-Wave Timeline--
2000 -
Darkhold: Blade #1, "The Last Drop"
-----------------------
2000 -
Blade II
2002 -
Blade II
2002 -
Spider-Man
2002 - Spider-Man: Teaser Trailer
2003 -
Hulk
2003 -
Ghost Rider: Extended Cut
2003 -
Daredevil: Director's Cut
2003 -
The Punisher: Countdown #1
2003 -
The Punisher: Extended Cut
2003 -
Spider-Man: The New Animated Series 1x01, "Heroes & Villains"
2003 -
Spider-Man: The New Animated Series 1x02, "Royal Scam"
2003 -
Spider-Man: The New Animated Series 1x03, "Law of the Jungle"
2003 -
Spider-Man: The New Animated Series 1x04, "The Sword of Shikata"
2003 -
Spider-Man: The New Animated Series 1x05, "Keeping Secrets"
2003 -
Spider-Man: The New Animated Series 1x06, "Tight Squeeze"
2003 -
Spider-Man: The New Animated Series 1x07, "Head Over Heels"
2003 -
Spider-Man: The New Animated Series 1x08, "The Party"
2004 -
Spider-Man: The New Animated Series 1x09, "Flash Memory"
2004 -
Spider-Man: The New Animated Series 1x10, "Spider-Man Dis-Sabled"
2004 -
Spider-Man: The New Animated Series 1x11, "When Sparks Fly"
2004 -
Spider-Man: The New Animated Series 1x12, "Mind Games, Part One"
2004 -
Spider-Man: The New Animated Series 1x13, "Mind Games, Part Two"
2004 -
Spider-Man 2.1
2004 - Spider-Man 2: News Report
2005 -
Hulk
2005 -
Hulk: Gamma Games #1-3
2005 -
Man-Thing vol. 4 #1-3
2005 -
Man-Thing
2005 -
Spider-Man 3: Movie Prequel #1
2005 -
Spider-Man 3
2005 -
Spider-Man 3: The Black #1
2005 -
Spider-Man: Friend or Foe
2005 -
Fantastic Four: Extended Edition
2005 -
The Punisher
2005 -
Elektra: On the Rise #1
2005 -
Elektra: Director's Cut
2006 -
Blade: Nightstalking #1
2006 -
Blade: Trinity: Extended Version
2006 -
Blade: Day Walker vs Vampire Hunter #1
2006 - Blade: Blood Thirsty
2006 -
Blade: The Series 1x01/1x02, "House of Chthon"
2006 -
Blade: The Series 1x03, "Death Goes On"
2006 -
Blade: The Series 1x04, "Descent"
2006 -
Blade: The Series 1x05, "Bloodlines"
2006 -
Blade: The Series 1x06, "The Evil Within"
2006 -
Blade: The Series 1x07, "Delivery"
2006 -
Blade: The Series 1x08, "Sacrifice"
2006 -
Blade: The Series 1x09, "Turn of the Screw"
2006 -
Blade: The Series 1x10, "Angels and Demons"
2006 -
Blade: The Series 1x11, "Hunters"
2006 -
Blade: The Series 1x12, "Monsters"
2006 -
Blade: The Series 1x13, "Conclave"
2006 - Blade: Trinity: Alternate Ending
2007 -
Ghost Rider
2007 -
Fantastic Four: Rise of the Silver Surfer
2008 - Iron Man: Alternative Ending
2011 -
Ghost Rider: Spirit of Vengeance
2012 - The Punisher: Dirty Laundry
2016 -
Deadpool
2016 - Sky Fibre and X-MEN Apocalypse TV Ad - Extended Cut
2017 - No Good Deed
2018 -
Deadpool 2: Super Duper $@%!#& Cut
2024 -
Deadpool & Wolverine
2024 -
Spider-Man: No Way Home
2026 - Laura.mov
2026 -
The New Mutants
2026 -
The Marvels
2029 -
Logan
Just for fun, obviously this isn't a legitimate universe.