Spider-Man 2099 has appeared in the following comic books:
2099 A.D.
2099 A.D. Apocalypse
2099 A.D. Genesis
2099 Sketchbook
2099 Unlimited
2099: Manifest Destiny
2099: World of Tomorrow
Age of Ultron
Avengers
Avengers Academy
Avengers Forever
Battlezones: Dream Team
Beavis and Butt-Head
Captain Marvel
Doom 2099
Fantastic Four 2099
Ghost Rider 2099
Marvel Age
Mega Marvel
Punisher 2099
Ravage 2099
Spectacular Spider-Man Adventures
Spider-Man
Spider-Man 2099:Volume 1 Issues 1-46, Volume 2 Issues 1-present
Spider-Man 2099 Meets Spider-Man
Spider-Man Family
Spider-Man Family Featuring Spider-Clan
Spider-Man Family Featuring Spider-Man's Amazing Friends
Superior Spider-Man
Superior Spider-Man Team-Up
The Amazing Spider-Man
The Astonishing Spider-Man
The Exploits of Spider-Man
The Marvel Masterpieces Collection
Thor Corps
X-Men 2099