Well, I've let your ideas stew a bit and I think I've come up with a direction to go in. I also read up on Cube and 13 Ghosts (haven't had time to rent and watch them, but I definately want to see Cube sometime.)
I'm thinking the Gears is ALL of the things that have been mentioned. (No, this isn't a copout, bear with me.)
The Gears started out long ago much like ScS's Babbage demon. It's a sentient entity, hungry for knowledge and yet seemingly all-knowing. But after its first creator was killed, it lured in another, pehaps Daffy's gnome, who expanded the machine and created another Room within it. This one was meant as a trap for the Talons, and perhaps it worked, perhaps it got the gnome killed. Either way, having it's "brain" altered by a different craftsman gave the Gears another perpective, and opened its growing mind up to new experiences. More than just knowledge, it now craves
ways of thinking, and the path for it to gain them is more craftsman, each one filling out a new Room with clockworks for their own goals.
The more Rooms that were added over the years, the smarter and more alien the mind of the Gears became, until one day it was insightful enough to deduce the existance of Mechanus, the clockwork plane of pure Law, and it naturally felt drawn to this place. It's new goal was to become its own portal to Mechanus, by transcending thought, space, time, and the Dark Powers. And it would only reach this divine level of enlightenment when "complete" with 13 Rooms, built by 13 mechanical geniuses. (Thank you Mortavius, and 13 ghosts)
Somewhere along the way, the Rooms themselves became mobile within the werehouse (sic), running on cranes and tracks, twisting and turn as thoughts and connections are made in the Gears's mind. (Thank you, Daffy and Cube)
Gustav is one of the 12 genius who have built rooms so far. As DeepShadow said, he was inspired by the existing rooms, but he was also compelled to add his own. His was a trap for Talos, much as the gnome's was a trap for Talons. This is where the music will play that is Talos's Zeitgeiber.
Another room may be the remnants of Jasper's hive of Sheens.
Another room is a divination room, a la BlackBox Gamer. (I'm actually picturing a a clattering "Tarroka Screen." Like those clattering displays at the airport or train station showing arrivals and departures. Built by a scholar trying to "break the code" of Vistani divination.)
I'm sure my Fir would fit somewehre in a room, too.
This idea gives me the benefit of using all the ideas at once, while also givign each room a flavor, to build traps on. And the opportunity for Gustav's apprentice to build Room 13.

"We're realistic heroes. We're not here to save the world, just nudge the world into a better place."