I prefer running in the evening or at night. I think it is a great way to wind down my day. Plus, it also gives me something to look forward to those last few hours of work.
Occasionally I wake up early to go for run, but it never feels as good as it does after work. Like most runners and other early morning exercisers, I just figured I was "still waking up" and according to NY Times' Gina Kolata that is close to the explanation. Apparently, we (humans) are better at working out later in the day, generally speaking, of course.