how to rust rail tops

The only thing I can think of that would work ok is to use a "Blacking" agent on the tops as it conducts electricity.  Any paint put on top would render it useless to engines (though that would be a cool way to park cabeese without their lights burning).  So the only option I can think of is to clean the rail tops really well and use a blackening agent.  

I don't know of any metal oxide that will conduct electricity AND look like rust.  You could try using copper foil to cap the track and then "weather" it with graphite or Neolube (which is graphite in a suspension that can be brushed on).  This stuff is slippery, the copper will still oxidize and result in loss of conductivity, the track will arc like crazy anyway.

I think this one is up there with how to make black smoke.

I know this isn't the answer that you are wanting, but one solution is to use actual rusty track.  Of course, you will need to power the trains in some other manner than electrical pickup from the rail... perhaps onboard battery power.  The O34 loop on my clockwork layout is naturally rusty Marx track, which I bought for a pittance since it was useless for electric trains.  The windups are slowly polishing a thin strip on the top and inside of the railhead.  A side benefit is increased traction, at least until the rust is worn smooth.  The clockworks do not, however, put out black smoke... 

I'm with Jumijo on this one.  Painting or otherwise "weathering" the sides of rails is certainly fine, but few and far between are the hobbyists who would want to do the same to the railheads, aside from track sections designed to represent abandoned trackage.

As noted above, a solid line of rust on the top of the rail would be impractical. However, and this will require a ruler and some planning, you could place splotches of rust on the track. Take note of the engines you'll be running on this section of track and the spacing between the pick-up rollers and which wheels are wired to the common. You would want to make sure both common rails are wired.

There are a couple of downsides to this method. First, an engine with one pick-up roller would not work. Second, you would risk spreading contamination if the rust splotches aren't sealed in.