I commute and given my work schedule, night riding is just part of the package. Obviously, an investment in a good lighting system is important. I have a helmet light AND a handle bar light. The handle bar light is more back up than anything or for those odd occasions when I've got caught out later than I thought I'd be. Back blinkie a necessity. I consider a fully charged cell phone a necessity.
I stick to the roads and stay off the trails, working on the theory that if I fall off my bike, and get hurt, I'm more likely to be seen on the public roadway than on the trails which are pretty deserted. Between the hours of 1 am and 3 am, I tend to drive on the sidewalk rather than on the main road, which I know is a No-No, but I'm competing for road space with drunks.
Personally, I've never had an encounter with a yahoo but I've had a couple of friends who got grief from the jerks. Again, a reason for me to stick to well travelled public roadways at the dark hours.
I also let my co-workers know which route I'm taking home and I call when I get there so they don't send the search party out after me.
On that note, I've gotten to the point where I love my late night rides. Part of my ride parallels the Nashwaak River and I have beautiful memories from this summer of biking along it, full moon and just me and my bike. Very peaceful.