Graphene has been a subject of intense interest because of its unique physical properties. Raman spectroscopy became a valuable tool for determining the number of graphene layers and assessing their quality. Here we review our recent results on the effects of substrates and temperatures on Raman signatures of graphene. Specifically, we considered graphene on GaAs, glass, sapphire, standard Si/SiO2 substrates and suspended across trenches in Si/SiO2 wafers. We found consistent values for Raman G peak frequency in the suspended graphene and graphene on standard substrates. It was relatively strongly down-shifted by ∼5 cm−1 for graphene on A-plane sapphire. Raman inspection of many spots on graphene layers on glass indicated that in some instances G peak was split into doublets. We investigated the temperature dependence of the Raman spectrum of graphene and found that G peak red shifts with increasing temperature despite graphene’s negative coefficient of thermal expansion. Using the measured temperature coefficient of graphene G peak we were able to adopt Raman spectroscopy for determining the thermal conductivity of graphene. The knowledge of the temperature and substrate effects on graphene Raman spectra is important for extending the application of micro-Raman spectroscopy as a nanometrology tool for graphene characterization and graphene device fabrication.