It seems to be part of the suit. As his red eyes started in X-Force: Sex and Violence #1. I guess the artists just wanted Wolverine to look more sinister. Than again if you are reading the new Wolverine saga the red eyes might play in to that. Can't say anymore without spoiling the story.
This weeks reading list:
Batman #703
Batman and Robin #14
Batman Odessey #3
Amazing Spider-Man #641 (Conclusion to One Moment in Time)
Amazing Spider-Man #642
Daken: Dark Wolverine #1
Daredevil #510
Shadowland: Blood on the Streets #2
X-Force: Sex and Violence #3 (Conclusion)
X-Men: Curse of the Mutants #3