Strobe lights on cab roof what are the guidelines for use?

The answer depends on the era, location (city/state) and particular railroad. In general, for a U30C in the 1970's, an amber strobe light would be on all the time for a lead unit on the road. It would be off when parked in the yard or if it is a trailing unit. (It was not unusual in the 70's on the BN to see the cab beacons illuminated on multiple units, however.)

Currently, I occasionally see white strobes on Amtrak and Sounder lead units when operating in poor visibility conditions, i.e. fog, rain, snow etc. 

The Western Maryland and Chessie System both experimented with beacons/strobes on some of their EMD locomotives.
In the late 1960s WM put rotating yellow beacons on 2 of their SD35s, but these were not successful and were taken off when the engines were shopped and repainted in the early 1970s.
Chessie experimented with white strobes, similar to those used on emergency vehicles of that era. Along with several orders of GP40-2s delivered in 1978, about 14 of WM'S 2nd-generation EMD's (GP35,SD35,GP40) got the strobes about the same time.
These strobes on the cab roof were activated by ringing the bell, which made them primarily for grade crossing visibility. They were eventually removed by CSX.

I have seen most remotely operated units with yellow strobes, I think they are on when engine is running.

Marty

I would research the particular road or engine you are modeling. On my 1970s BN stuff I have dummy stobes on all of them as per the prototype engines.  

I have mixed feelings about strobes. I believe they enhance ssfety for motorists and civilians, but are disorientating and annoying to crew. Especially in fog and rain. They can be more than annoying. They can actually ruin night vision. And induce siezures under some circumstances. Certain people are more susceptible to this effect. I believe they should be installed but used judiciously. They can be a pain-in-the-neck in small aircraft in fog and rain, though a boon to visability. A great idea for materials handling equipment at trackside. And in street running. I think use should be determined by the engineer. That should be the rule. Some people are really bothered by them, especially the reflections.  The mounting and shielding are critical. In most cases they are too far foward. Mechanical rotating lights are a maintenance nightmare.

The RF&P switchers operating Potomac Yard had them, so that the dispatcher in the tower could see where they were in the vast yard.

I never liked the look of them.  This old USAF locomotive has one.   

Most Frisco engines had yellow beacons...they were turned ON continuously.

They annoy me on my models when ya can't shut em off too.

I think they're a good thing especially on a branch line where there are many unprotected crossing (no gates or flashers just cross bucks)    They do attract one's eye.