There was at least one old adventure (pre-3E) that took place inside a body. It might have been from Ravenloft. Does anyone remember what it was called?
In Planscape's Dead Gods part of the adventure is inside a dead god. Earthshaker you are in the giant body of a huge robot. Those are the only two I can think of off the top of my head.
That was also the premise of a D&D2E module that the RPGA ran back around 1996 or 1997. It was on the theme of "Fanstastic Voyage", with the party having been super-miniaturized by a wizard. I believe it was written by either Roger Moore or Skip Williaims (I was the RGPA coordinator for several cons back then).
Nightmare Keep is the one I was thinking of, but I'll check them all out if I can find them. I'm looking for maps of a dead god's body for my game, and they all sound like they'll work.
An actual dead god, or its avatar? Check out the module called Earthshaker. It was a mechanical/steampowered/magical giant metal humanoid. You had to fight it from the inside.
Actual dead god. The body of a dead god of magic is floating in the astral plane and the thing the PCs are after is inside it. I'm mostly just looking for maps, as the body's primary defenders will be oozes made from the Living Spell template (it's a 3.5 game).
Of course, any other cool ideas I can pilfer from the modules will be welcomed.