I very much like the thematic link (mabye because I love constructs) but the complexiy golem seems a bit out of place here. The other two are very concrete representations of unreal things (dreams and the idea of a dungeon as one enemy) but it seems to be an unreal representation of an equation that may well be real (kinda). It also feels a bit forced compared to the other two.
On to the good. I have always wanted a mastermind benind a dungeon that could interact with it, and the brain is just that. I imagine it in combination with the dungeonmaster prestige class (I think from dungeonscape) as the ultimate dungeon-lord, or as part of a haunted castle. I would consider making a variant that could share abilities it had with its dungeon and be able to manipulate the dungeon more directly, effectively using the dungeon as its body.
I like the template, but can't currently think of a great use for it. If you could post some more adventure ideas with it, that would be great.