If your tracks are already down, and you don't have an air-brush, try a brown permanent ink marker (with a small tip). I found one at Michaels (can't remember the brand right off), and it worked pretty well. Of course (in hindsight) the best time to do this is before the track is laid.
I plan to lay, wire and test my track and then weather the rails using a spray can of Floquil roof brown before I put down ballast or do any other scenicing. This is the way it was recommended to me that sounded most logical.
I wondered about how I would manage that. Does that work pretty good? One person told me to put some sort of oil on a Q-tip and wipe the top of the rail head with it before painting...supposedly the paint won't stick to it and you can come back and wipe it off with a paper towel on a block of wood.
How did the brown marker work out? I need to get my track weathered so I can start on ballast. Not sure I want to use the spray paint because of ventilation issues.
There are several items to consider about the best way to weather rail and/or ties. Is an airbrush available? This is the best way to spray paint on the rails after they are laid down and ballasted. Gives you the most control. You can spray the rails one color and the ties another. Remember that everything doesn't weather the same. Rail will weather unevenly in shades. Ties will bleach out diferent from tie to tie. I have tried both the spray can and felt tip markers for putting color on rails. I would give the felt tip marker a little edge over the spray can method for weathering rail. This is because the marker gives you a lot of control in the application of color. With using a spray can the color goes all over and you have to take steps to control your overspray. I would recomend checking back issues of MODEL RAILROADER, N-SCALE, AND RAILROAD MODEL CRAFTSMAN magazines. There have been a lot of articles dealing with track weathering in these magazines
After laying, wiring and testing the track, I spray the rails with the airbrush. After ballasting, I spray over the whole track and ballast to give the amount of weathering desired, different amounts for main lines or sidings, etc. I have tried the 'oil on railhead' method, but usually forget, and have to remove the paint afterwards, either by cleaning fluid, or abrasive rubber (bright boy or similar). Painted track is quite easy to do, but adds enormously to the realism, so is well worth the effort.
