We present a systematic study of the Cherenkov radiation of Josephson plasma waves by fast moving fluxon in a stack of coupled long Josephson junctions for different fluxon modes. It is found that at some values of parameters current-voltage characteristic may exhibit a region of the back-bending on the fluxon step. In the opposite limit the emission of the Cherenkov radiation takes place. In the annular junctions of moderate length the interaction of the emitted waves with fluxon results in the novel resonances which emerge on the top of the fluxon step. We present more exact formulas which describe the position of such resonances taking into account difference between junction and non-linear corrections. The possibility of direct detection of the Cherenkov radiation in junctions of linear geometry is discussed.