"Great" is probably too strong a word, but there is no question that physical activity of any type burns calories, including fidgeting. I wouldn't use it as a substitute for exercise, but even just sitting there tapping your fingers or straightening things on the desk is better than doing nothing.
Often times when people are bored they will bop a knee up and down or tap or wiggle a foot, and this can mean anything from being anxious to boredom to movements to burn more calories. I think if you are fidgeting due to stress, it may not burn more calories, but instead it may burn calories, but also cause other issues. I say fidget to music to burn calories, especially if you are sitting at a desk all day!
Fidgeting is a way to burn a minimal amount of calories, but it is in no way an effective weight loss routine. The energy spent fidgeting can be put into much more productive activities for burning calories, such as walking, swimming or dancing, which are all great additions to a weight loss program.
To say that fidgeting is a great way to accomplish anything is a stretch. One may successfully burn calories by fidgeting but they are likely to burn bridges as well. Toe tapping, pen spinning, and seat squirming are distracting activities that are probably more likely to drive more people away than pounds.