Boss

In video games in general, a boss is a particularly large or difficult computer-controlled character that must be defeated at the end of a segment of a game, whether it be for a level, an episode, or the very end of the game itself.

Doom/Ultimate Doom
The bosses of the Ultimate Doom episodes are:

Doom II/Final Doom
Doom II and the games based on it all have the same boss:

(MAP30: Last Call can be completed without killing the boss in Deathmatch.)

Doom 64
Bosses in Doom 64:

Heretic
Bosses in Heretic: Shadow of the Serpent Riders:

Hexen
Bosses in Hexen: Beyond Heretic:

Strife
Bosses in Strife: Quest for The Sigil:

Special effects
In most of the levels above, defeating the boss monster(s) causes the level to end. In E1M8: Phobos Anomaly, however, killing all the Barons lowers all walls with tag 666. In E4M6: Against Thee Wickedly, killing the Cyberdemon causes a metal grate (four columns with tag 666) to blaze open, providing access to the exit switch.

The same function (A_BossDeath in p_enemy.c) is used in MAP07 of Doom II-based games to lower floors with tag 666 when all mancubi have been killed, and to raise floors with tag 667 when all arachnotrons have been killed. Similarly, in MAP32 (but using a different function), killing all the Commander Keens causes doors with tag 666 to open. Thus, these monsters can be considered bosses in the levels for which they play a special role.