The critical slowing down of the usual Markov chain hybrid Monte Carlo algorithm has become a serious limiting factor in current lattice QCD calculations, especially those using chiral fermion formulations. We will discuss the application of generalized Fourier acceleration as a potential solution. Both a fixed-gauge approach using standard Fourier acceleration and the Riemannian manifold hybrid Monte Carlo based on the eigenmodes of the covariant Laplace operator will be discussed and results of numerical experiments presented. These include studies of 4D SU(3) gauge theory with a variety of actions and some first results including quarks.