Just a heads-up that these are still coming out. This thread might be better suited to the actual comics sub-forum, but it's a television show and some of you guys who follow Heroes might not notice it over there since the first page of threads in comics has threads that haven't been active since the 23rd of November 2007.
I'll go back and link to season 1 at a later point, but here are the ones that ran with season two, and are still going right up to one released today, starting at issue 52:
52: Flying Blind: Introduction to West, a classmate of Claire's at Costa Verde High School.
53:
The Crossroads: What did the Haitian do before leaving Haiti?
54:
Petrified Lightning: Something so deep in nature. Peter learns the tale of Cúchulainn.
Bonus:
The Rogue: Derek steals Claire's car and drives to Mexico.
55:
The Trial of the Black Bear: Takezo Kensei and Hiro Nakamura try to obtain a scroll from the Black Bear of Sakashita.
56:
Molly's Dream: An exploration of one of Molly Walker's comatose nightmares.
57:
Team Building Exercise: Noah Bennet's first "bag and tag" mission with the Company.
Interactive Novel:
The Last Shangri-La: Hana sends an associate to Bhutan in search of a long-lost relative. Continuing events from Heroes Evolutions, this is the first graphic novel presented exclusively in Flash.
58:
Quarantine: Homeland Security official Howard Lemay deals with the devastation of the Shanti Virus.
59:
Man on Fire: D.L. Hawkins becomes a different kind of hero.
60:
Revolutionary War, Part 1 - Pursuit: Adam Monroe meets his match.
61:
Revolutionary War, Part 2 - Pursuit: Adam Monroe learns a lesson from Evan.
62:
Special: The backstory behind West's abduction as a child by HRG and the Haitian.
63:
Elle's First Assignment, Part 1: Elle's first assignment from the Company.
64:
Elle's First Assignment, Part 2: Elle continues her assignment from the Company.
65:
Normal Lives: Noah Bennet tries to live a normal life.
66:
The Ten Brides of Takezo Kensei: Adam Monroe recounts his past loves while buried alive.
67.
The Golden Goose: Bob Bishop attempts to find the enigmatic Richard Drucker.
Sometimes worth it just for the bonus pic that comes at the end of each comic.
See, Adam agrees.