I agree with Mr Don Modesto regarding getting the muscles warm before stretching.
Our warm up routine incorporates some light jogging and/or basic movements (irimi and tenkan), followed by fune kogi undo or ikkyo undo or some other breathing exercises to generate some ki and energise the body. This is followed by stretching, ukemi and shikko (sp?). The routine takes about 20 to 30 minutes. There is about an hour of instruction followed by a cool down of about 10 minutes.
As for a personal favourite, I like doing fune kogi undo or ikkyo undo. I feel quite warm and ready to train.
Happy training all