I have certainly noticed exercise having a positive effect on my mental well-being. My first year of graduate school I was a real couch potato and fast food junkie. This year I decided to change my lifestyle, and I set a goal of finishing a sprint triathlon in the spring. I feel immensely better about myself, and I certainly feel much better physically. When I am facing a difficult problem at school and can't seem to figure it out, I just go for a bike ride (big problem) or a run (smaller problem), and I usually have some fresh ideas by the time I'm done. Also, I find that morning exercise precludes the need for caffeine in the morning, providing even more health benefits.
Incidentally, finished my first triathlon two weeks ago, and I'm officially addicted!