Sirius, Snape and the "Prank." Lupin's and Sirius' behavior in the Shrieking Shack
Hints of darkness to Lupin's personality which, even apart from his lycanthropy and consequent social standing, might have contributed to his friends' suspecting him of being the spy during Voldemort's first rise.
The warrior culture of the wizarding world, and how it militates against apology. An analysis of Lupin's response to Sirius' plea for forgiveness in the Shrieking Shack and why it might be that so many readers feel some degree of discomfort or dissatisfaction with that exchange.
Analysis of the scene in PoA in which Snape brings Lupin his Wolfsbane Potion
More on why Sirius and James might have suspected Lupin of being the spy, this time with an emphasis on his lycanthropy. Evidence from the Shrieking Shack scene to support the notion that Sirius, at least, really did suspect Lupin primarily because he was a werewolf. Also, a brief discussion of the canonical plausibility of Evil!Lupin, and an explanation of why Sirius and James might not have suspected Peter.