As of 22 November 2014, here's a list of bosses that can appear in normal boss battles:

Special bosses

These types of bosses are generated on-the-fly. They can be disabled in system.dat, but if not, there's a chance that a special boss will appear instead of normal bosses.

Doppelgangers (level 10-75)

Evil doppelgangers of the players in the battle will appear to fight them. Use your knowledge of yourself and each other to win.

Monster Warmachine (level 10-300)

The monsters build a large tank-like warmachine to fight the Allied Forces. There are three warmachines. One is selected depending on the level.

Bandits (level 100+)

A bandit leader and a number of minions will fight the heroes.

Crystal Shadow Warrior (level 16+)

Conventional tactics will not work against the Crystal Shadow Warrior. This battle will require thinking outside the box to win.

Pirate Ship (level 10-1000)

Similar to the bandit gang, a pirate leader and minions will attack, but one of two special bosses will appear when the leader is defeated.

Demon Wall (level 301-600) / Wall of Flesh (level 1001-5000)

The heroes will be brought to a special hall battlefield and forced to battle the demon wall. They will only have 15 turns to defeat the Wall, before it crushes them at the end of the hall, though Holy Aura can still hold the Wall back.

Elder Dragon (level 601-5000)

A special randomly-selected Elder Dragon will appear to attack the heroes.