Tsuchiyaa and Adolphs offer a review of brain structures central to emotion and consciousness, and how they overlap in several areas. (Trends in Cognitive Sciences, Volume 11, Issue 4, April 2007, Pages 158-167. PDF here). Here I reproduce their useful summary of the time stages in emotional processing.
Microgenesis of emotional processing. Emotional responses span a large temporal range (from 100 ms or less, to minutes). (a) Responses to emotional visual stimuli can occur rapidly in prefrontal cortex  or amygdala, in part mediated by subcortical inputs. Emotional response in the amygdala also influences early visual processing and is modulated by volitional self-regulation. (b) At later time slices (100–200 ms), sensory cortices provide more detailed input to emotion-inducing structures like the amygdala. Two components that are important to face processing are shown: the superior temporal cortex (green), important for encoding dynamic information such as facial expression, and the fusiform gyrus (blue), important for encoding static information such as identity. (c) Once the emotional meaning of a stimulus has been evaluated by the brain, emotional responses are triggered in the body via projections from amygdala and medial prefrontal cortex to brainstem nuclei and hypothalamus (not shown), and are in turn represented in structures such as the insula. This figure emphasizes that what we refer to as an ‘emotion state’ throughout this article is in fact a complex set of processes that unfold at various points in time. Color key: black, primary visual cortex; blue, fusiform gyrus; green, superior temporal cortex; purple, insula; faint red, orbitofrontal cortex; solid red, amygdala; yellow, superior colliculus.