I couldn't leave it out there in the cold.
The smallest ones ought to be the size of a wagon.
They are essentially a mountain composed out of gigantic turtle shell on the outside, and gigantic turtle bones and assorted gigantic turtle organs on the inside, interspersed with rivers of giant turtle blood. They may be covered with additional soil, or even sedimentary rock. Normally, it would be sleeping and function as a regular mountain.
When awake, their feet, head and tail are pushed outward slowly, pushing aside any soil in the way. Sedimentary stone can prove to be a problem, and many gigantic turtles die this way after an extended hibernation, the duration of which increases with their age - they're otherwise immortal. Such shells should be rare according to their size, and a living gigantic turtle should be even rarer. Their diet consists of plants and sand - to get minerals to grow their shells.
Digging into a turtle would awake it. Continuing to dig into it would kill it. As dwarves are far faster diggers than a giant turtle can try to seek relief for the pain in the water, it would be easy to kill. After that it's just a giant turtle shell filled with soon-to-be rotting gigantic turtle meat, however. Once it moves around, it breaks all structures connecting it to the surrounding landscape if it is strong enough. With every step, all structures left on it are subjected to a small earthquake.
Foreseeable problems:
The obvious one: defining a creature as a 3d group of tiles. As soon as that's done, however, hibernating gigantic turtles would not be a problem. Having them move around would require smoothly moving and recentering the map. If in fortress mode, there might be the option to split off a group of dwarves and declare the turtle a new fortress.
Since turtles move so slowly, that wouldn't be a big problem: just wait until there's room and then shift one appendage a square, or if possible push. After 3 appendages have shifted, shift the shell. Repeat.
It's rarity would be commensurate with it's size, however. Which means that the chance that two of them would mate in-game is virtually nihil.
Edit:
This one came up in the underground diversity thread, here:
http://www.bay12games.com/forum/index.php?topic=22308.msg384436#msg384436There's a topic in the eternal voting list now.