The em is the base metric, but is not based on any specific horizontal or vertical font feature (and neither is it the font height, which is WinAscent+WinDescent), but rather the em is for scale. For instance in 16ppem the em size is 16 pixels. The units per em determines how many units the em is, and it affects the process of fontdevelopment. What em size do you tend to use? Among TrueType font designers it is common to use 2048 units per em and among PostScript font designers it is common to use 1000 units per em, however it is possible to use any units per em in fontdevelopment. For instance, it might be possible to use 256 units per em. In fake bitmap fonts the em size will likely be a multiple of the bitmap em size in pixels (not necessarily the bitmap font height).
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