Timing a work out to get optimal results is uber important. Unfortunately, there are about a billion different opinions on workout optimization. Here is what I have learned, dumbed down and put into a teeny tiny nutshell.
Exercising in the morning will boost your metabolism for the rest of the day. This is why you feel a little more chipper on the days you work out in the morning. If you are feeling run down in your day, it may be because you are overworking your body. This is something I was doing a lot until I got a heart-rate monitor. Your heart rate should stay between 65%-85% for about 30-45 minutes for a solid workout. Anything higher and you could be damaging your body more than helping it. This is partially due to an increase tissue recovery time and partially due to burning muscle and fat when you go above 85%.
Although you should stay in your aerobic heart rate zone for long durations. There are times when your heart rate can go higher than 85% to build power and muscle. This should not be done for more than two minutes at a time. More than 2 minutes and you will feel fatigued, plus your muscles will feel sore from an overproduction of lactic acid.