PLAYPAL

A PLAYPAL is really a collection of palettes used for various purposes. It has a total of fourteen palettes, each 768 bytes. Each palette has 256 colors of three unsigned bytes each (0-255); one for each of red, green and blue. Furthermore, the COLORMAP resource also affects the display of colors on screen.

The palettes each have a specific function: An examination of the Doom source code reveals that the unused palettes (1 and 9) were likely intended to be the first levels of the red and yellow tinting effects. Because of the logic used in the palette code, they are never used.

Tools which can be used to manipulate the PLAYPAL include Inkworks and DeePsea.

Hexen
In Hexen, the engine uses an extended PLAYPAL lump containing 28 palettes, of which the additional palettes are used for several new effects.

Index 247
Many specialized editing tools (notably NWT, SLumpEd and XWE) rely on the assumption that palette index 247 is not used and can safely be used as a "transparent color", which they display as cyan because it contrasts well with the rest of the Doom palette. This assumption, however, is incorrect. Palette index 247 is used by some Doom II graphics, and it is black (0, 0, 0), not cyan. All 256 colors of the palette are shown in the patches and sprites picture format, as a different mechanism for transparency is used. Palette index 247 is used even more in other Doom engine games such as Hexen. The mistaken assumption created by having these tools treating cyan as a transparent color when importing pictures and converting them to Doom-format graphics, or by giving transparency to pixels indexed 247 when exporting, results in many problems: patches and sprites exported from the IWADs might have "holes" that they shouldn't have, and attempts to actually use cyan as a color in graphics (with a palette that does contain this color) are hindered.

Source

 * This information is from the Unofficial Doom Specs.