A recent study in The Journal of Strength & Conditioning Research (2010; 24 , 2274-79) suggests that static stretching before exercise may adversely affect performance. The study participants, ten collegiate male athletes, were evaluated for their performance on two different occasions for a 60 minute treadmill bout. The athletes performed static lower body stretches for 16 minutes prior to one of the runs. Before the other run, they simply sat quietly for 16 minutes.
The authors of the study found that "performance was significantly greater in the nonstretching vs. the stretching condition, with significantly greater energy expenditure during the stretching compared with the non-stretching condition." It's likely that stretching before exercise stimulates "protective mechanisms" within the muscle, overriding muscle spindles (sensory receptors that detect changes in muscle length and play an important role in regulating muscle contractions).
So, if you are somebody who likes to combine exercise with yoga or a stretching routine, start with exercise and conclude with stretching.