Hmm... ok, so there isn't anything out there like this. I think a design doc is in order. Real Tron, lol.
Just off the top of my head, I'd say that conditionals would be represented by semi-transparent connectors with the texture of the originating object. I was thinking that the individual faces of polyhedrons could be a generic "container" for functions, methods, definitions, etc.
The usefullness would be the ability to visually design an application by dragging, dropping, linking, and texturing code objects without a greater understanding of the code beneath. Some sort of AI would have to make assumptions on what specific linkages are supposed to mean in the source code itself.
For instance, let's say you grab a textbox cube, place it in the application space, then switch to form view, place it correctly on the form, where you want it to be, and then back to 3D design. Add a text display object, then use an Output shaded line to link from the textbox to the display object. The program would assume that on an event, the contents of the text-box would be presented in the display object.
To modify the event, right click on the linker object, which would present you with the properties of the methods available to the textbox object. Set your Event as the Enter key, or some such.
An AI would have to be designed to make assumptions based on the visual logic of the designer. All those assumptions could be run through an interface of some sort that lets you choose the "settings" of an object being placed or modified. Each "object" in oop by definition contains it's own context, so designing a tool to read that context meaningfully and determine possible interactions with another specific object should be possible.
An arbitrary set of spatial relationships could be defined on the fly, so as to keep the program manageable and uncluttered. Zoom tools and auto-occlusion would be all thats needed to focus on individual areas of code... imagine flying over a city, only the city is on the surface of a sphere. Or a Cube, or however. I imagine that once this program goes through the first few stages of testing and real thought/effort, the creators would come up with the solution to the problem of viewpoints and gestalt mapping.
Oh, and it would prevent any sort of dead zones in your code. I know I've had that problem before... code that appears to be functional and integrated with the project you're working on, but through some sort of error, the code is isolated from any real interaction with the rest of the program. Faulty interfaces and flow control would be presented in a visual manner, while the actual code remains a black box to the user. Unless you want to view it, of course, but thats the idea.
Anyway, lots of good thoughts. I'd love a tool like this, especially with an import function to bring in and automatically parse existing code into 3D objects.