There are many comic book series, published primarily by Marvel and Devil's Due, set in G.I. Joe's A Real American Hero continuity. These include:
G.I. Joe A Real American Hero
G.I. Joe A Real American Hero by Devil's Due, also known as Reinstated
G.I. Joe: America's Elite
G.I. Joe: Battle Files
G.I. Joe: Data Desk Handbook
G.I. Joe: Declassified
G.I. Joe: European Missions
G.I. Joe: Frontline
G.I. Joe: Master and Apprentice
G.I. Joe: Master and Apprentice 2
G.I. Joe: Order of Battle
G.I. Joe: Special Missions
G.I. Joe: Special Missions by Devil's Due
G.I. Joe Special
G.I. Joe Yearbook
Dreadnoks: Declassified
Scarlett: Declassified
Snake Eyes: Declassified
Storm Shadow
Tales of G.I. Joe
The Hunt for Cobra Commander
There are also Transformers-related events within this continuity, but they are ignored in the Devil's Due fiction:
G.I. Joe and the Transformers
Transformers: Generation 2