The only way to stop on your bike is to apply both brakes as necessary, before you come to a complete stop release the front brake and use back brake to bring the bike to a smooth stop (if you continue to use front brake you will cause the front end to jerk as the front forks take the final braking strain...which isn't great for control purposes). When you release the front brake and you have the back brake applied, pull in the clutch when you have to!! and keep back brake covered while the LEFT leg goes to ground to keep the bike stable. This is the ONLY way you should ride your bike as it is the safest. If a car threatens to rear end you then you have a good chance to get away as you are still in first gear and you just have to move off as normal. Also if a car does rear end you, chances are you wont be thrown over the handlebars as the front brake is not applied. You will move forward and fall off but as your not thrown over the handlebars there is less risk that the bike will fall on top of you and crush you to death. Finally, it is NOT bad on the engine to keep the clutch pulled in for long periods, but if you find that a few cars have come to a stop behind you it is safe then to apply front brake, pur right foot down, bring left foot up to knock bike into neutral, put left foot down to ground, bring right foot back to the rear brake and release the front brake. Just do the reverse when the lights are about to turn green.
I know some of you will say this is rediculous but this is the correct way to ride your bike. Its a pain in the arse with all the foot switching but you will find that any descent motorcycle Police officer/ cop/ Garda will do this. I was taught this by a man who instructs the UK police how to ride at an advanced level.
EDIT: just noticed that what I have explained is in the post above!!

at least what i have said backs up the technique that every biker should know and practice!