Described systems and methods allow protecting a computer system from malware such as viruses, worms, and spyware. A reputation manager executes on the computer system concurrently with an anti-malware engine. The reputation manager associates a dynamic reputation indicator to each executable entity seen as a unique combination of individual components (e.g., a main executable and a set of loaded libraries). The reputation indicator indicates a probability that the respective entity is malicious. The reputation of benign entities may increase in time. When an entity performs certain actions which may be indicative of malicious activity, the reputation of the respective entity may drop. The anti-malware engine uses an entity-specific protocol to scan and/or monitor each target entity for malice, the protocol varying according to the entity's reputation. Entities trusted to be non-malicious may be analyzed using a more relaxed protocol than unknown or untrusted entities.