Before you say "but that means that there is less time for cars to cross the intersection", consider the fact that a lot of the people using bikes would otherwise have to use other means of transportation, resulting (at least partially) in reduced traffic.
For a lot of the less popular intersections, free for alls work good enough and trying to be clever would be a premature optimization. In other situations, there are generally two approaches:
* implement a more complex routing strategy that can route both cyclists and cars concurrently; an example would be [1], where the blue line is how the cyclist should travel.
* avoid the intersection al together with tunnels[2] or bridges[3] -- this is the most desirable strategy, but probably the most expensive one. It is used fairly often in popular-by-cycle cities such as Utrecht and Amsterdam.
[1] http://img122.imageshack.us/img122/3652/kruispunt2pz8.jpg
[2] http://www.n246.nl/wp-content/uploads/2012/02/4398.jpg
[3] http://www.provincie.drenthe.nl/publish/pages/72918/afbeeldi...
Regarding the lights - sure. Cars have a special light, pedestrians have a special light. Why wouldn't bikes? Having a usable bike infrastructure that doesn't make bikers feel like they're going to die at every intersection would promote safer biking. I'll run a red light on my bike because I can see the cars coming from my left and right, but I can't see the car coming from behind and turning right into me.
As somebody elsewhere said, if you get more people riding, you are removing their cars from the road, but there is a real chicken and egg problem, as drivers will be very upset if they see their commute lengthen.