Scientific findings of strobe lights and the brain
The presentation of flickering lights usually leads to so-called steady-state visual evoked potentials, that is, oscillatory responses in the visual cortex with the frequency of the stimulus as well as its harmonics. See for example: 

Herrmann CS. (2001)
Human EEG responses to 1-100 Hz flicker: resonance phenomena in visual cortex and their potential correlation to cognitive phenomena.Exp Brain Res 137(3-4):346-53.  Pubmed

There is a lot of research concerning this phenomenon. For a list of papers, please see http://www.ncbi.nlm.nih.gov/pubmed?term=steady%20state%20visual%20evoked%20potential