The solar wind is a significant component of non-orbiting particles in the solar system. It exerts a pressure on the order of nanopascals (at the radius of Earth; it gets stronger toward the Sun), which seems tiny but given that it acts constantly for millions of years is strong enough to slowly change the orbit of small bodies. Small bodies are more strongly affected because they typically have a larger cross-section to mass ratio. The effect on comets is particularly spectacular:
There are a couple of other sources of "friction" in vacuum. You mention gravitational waves in your question, and this effect is reasonably well covered in the answers to the question you linked. Another effect is dynamical friction. This one is a purely gravitational effect, so the term "friction" is a bit misleading. This illustration below sums up the effect nicely; as a massive body moves through a collection of other masses (could be a protoplanet moving through gas, a star moving through a field of other stars, a galaxy moving through a cluster of galaxies) it pulls some mass toward it, forming an overdense wake so that there is a net force opposing the motion.
The last effect I want to mention is radiation pressure (or photon pressure). Light actually exerts a slight pressure all on its own, which has an easily measurable effect on small solar system bodies, and is probably one of the best ways to try and save the Earth from a killer asteroid (forget nukes, use paint!). It's also the principle behind solar sails.