You can do that by scripting a dynamic light. And it depends on the approach, but yeah, I think you should give them different targetnames.
Back in Quake III days there was also this way of using the lightstyle string of a light entity to get such effects, don't know anything about it though.
maybe it was just my crappy vid card at the time but i swear city nights final's megapole map had flicker lights (neon) somewhere . also saturday night fever by caskami (II or III) has the old disco light dance floor . might want to look at those .
