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I'm thinking on a BBEG that worships two deities: A deity of war and constructs, and a deity of undeath. They believe that since constructs and undead are obviously superior to humans, then something that combines the best of both must be even better! To that end they have been manipulating others who worship either one god or the other into performing crazy experiments into combining the two. This ends up being a 3-phase fight:
Phase 1:
The players, of course, discover (and destroy) the true mastermind (a 20th level necromancer), whose soul is pulled into and begins powering/controlling their ultimate creation.
Phase 2:
This creation is actually 3 separate pieces, each of which can act independently. One piece is legs (waist down), which can only move OR attack (counts as staggered). Another piece is the arms and torso (waist up, but not head) which can make melee attacks and cast a limited selection of at-will spells (also counts as staggered). Last is the head, which has a stereotypical laser-beams-from-the-eyes attack but can also cast any remaining spells the BBEG had and has a plague breath weapon (which contains both disease and a con damaging inhalation poison).
The arms can cast Mass Harm, which heals itself for half (it's only half undead, after all) and hurts the party for full.
The bottom and middle pieces count as colossal size, the head counts as large.
If the head gets destroyed before the other two pieces do, the spell-casting ability from the BBEG moves to the arms.
Phase 3:
After destroying this form, pieces from it crawl out into a large-sized amalgamation of flesh and clockwork that has a grotesquely huge right arm (that wields a two-handed weapon complete with 1.5x str mod) whilst its normal sized left arm wields a tower shield. It also has access to any remaining spells of the BBEG (using a small arm on its shoulder to cast; this arm can be sundered [HP 50, hardness 20, vuln fire]), but retains any conditions and/or spell effects that the second form's head had on it. If the head was destroyed via some sort of disintegration effect (or otherwise destroyed utterly) than the third form fails to form properly (it's missing its construct bits), though the sight is utterly disgusting (and not quick) and will likely haunt the characters' dreams for years to come.
There you have it, my 3-phase (with justification!) boss fight.