What is the difference between EPM and APM?

Solution 1:

The notes for patch 1.4.3 state:

• APM values displayed on the Leader Board are now calculated by counting every click and command that has been issued by the player.
• EPM values displayed on the Leader Board are calculated by counting only actual commands issued by the player (Effective Actions Per Minute).

EPM is always smaller than APM since effective actions are a subset of all actions.
Time is measured in game time (aka Blizzard time), and it is not measured in real time.

As mentioned at a Team Liquid forum post, camera location commands (aka screen bookmarks) are not included in the calculations of APM and EPM.

Note that third party analysis tools often measure APM/EPM slightly differently to the Starcraft 2 software.

Currently (as of version 1.4.3.21029) there is a bug where EPM and APM values are reversed when viewing a replay. We should expect a fix sometime in a future patch.

Solution 2:

EPM = effective actions per minute is every valid action you make. So moving your marine will count but pressing a control group won't (Starcraft 2 default).

APM = actions per minute counts every click you make, like pressing a control group or moving a marine (old Brood War style). It should always be greater than or equal to EPM.

Note that (as of April 2012) these metrics appear reversed in replays.