What are reasons for a missed menstrual period, other than emotional stress, physical stress, and pregnancy?

Non ovulation. There are many reasons that a woman doesn't ovulate occasionally. Recurrent anovulation is usually associated with polycystic ovarian syndrome and can be treated with birth control pills or intermittent Progesterone or Clomid (clomiphene) if pregnancy is desired.
Normal variation. To occasionally skip a period should not be particularly concerning. The factors you mention are commonly asociated with irregular cycles. Polycystis ovarian syndrome (pcos) is by far the most common reason for irregular cycles.

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How much exercise or emotional stress can cause a missed or irregular period?

Worried you're preg? Overly exercising and high stress may cause an irregular period. Periods will stop if you are at a very low body weight, since body can not support a pregnancy. However, pregnancy might be the most likely scenario. I know you are uncertain but should have a home pregnancy test asap. Good luck to you. Read more...