I have been painting my rail and ties with a brush, but my layout is small and time is not an issue. I paint different ties different colors, and am quite pleased with the results. For larger layouts, I have used an airbrush or spraycan. I think floquil makes a "rail brown" color in a spray can that works well. I still reccomend brush painting a few ties a slightly different color to match prototype variation. Cleanup on railheads has never been an issue for me. I usually try to clean the paint off of the railhead with a paper towl before it dries, or with fine sandpaper afterwards. Model paint does not stick that well to unprimed metal (especially acrylic), so cleaning the rails doesn't take long.
kevin