We describe how color superfluidity is modified in the presence of color-flip and color-orbit fields in the context of ultra-cold atoms, and discuss connections between this problem and that of color superconductivity in quantum chromodynamics. We consider s-wave contact interactions between different colors, and we identify superfluid phases, with five being nodal and one being fully gapped. When our system is described in a mixed color basis, the superfluid order parameter tensor is characterized by six independent components with explicit momentum dependence induced by color-orbit coupling. The nodal superfluid phases are topological in nature, and the low temperature phase diagram of color-flip field versus interaction parameter exhibits a pentacritical point, where all five nodal color superfluid phases converge. These results are in sharp contrast to the case of zero color-flip and color-orbit fields, where the system has perfect U(3) symmetry and possess a superfluid phase that is characterized by fully gapped quasiparticle excitations with a single complex order parameter with no momentum dependence and by inert unpaired fermions representing a non-superfluid component. Furthermore, we analyse the order parameter tensor in a total pseudo-spin basis, investigate its momentum dependence in the singlet, triplet and quintet sectors, and compare the results with the simpler case of spin-1/2 fermions in the presence of spin-flip and spin-orbit fields. Finally, we analyse in detail spectroscopic properties of color superfluids in the presence of color-flip and color-orbit fields, such as the quasiparticle excitation spectrum, momentum distribution, and density of states to help characterize all the encountered topological quantum phases, which can be realized in fermionic isotopes of Lithium, Potassium and Ytterbium atoms with three internal states trapped.