Hi Katyrosh, great question... great timing too, I just published a hub on this topic this morning!
In summary, exercising in the morning can increase your metabolism (i.e. you will burn more calories over the day, even when you are not exercising). This may be good if you are trying to lose or maintain weight. However, people who are trying to lose weight often don't realize that research has consistently shown people tend to automatically increase the amount of calories they eat when they have done exercise. So the increased metabolism rationale only holds true for weight loss if you are regulating the type (and perhaps more importantly the portion size) of food you eat for the remainder of the day... otherwise the extra calories you burn will be offset by the extra calories you eat!
However, people who exercise in the morning are more likely to exercise regularly. For me, this alone is enough reason to exercise in the morning. I want to set up my exercise routine for success, it is easier for me to get sidetracked with other things in the afternoon.
People who exercise in the morning also report feeling like they have more energy for the rest of the day, and sleep better at night. Other health benefits of exercise will come to us no matter what time of day we exercise. The most important thing is to actually make sure we do it!
Here is the link to that hub if anyone is interested: