We want 3D datamining

At work we have this system...this big, huge 20-year-old system. Consisting of 1500 programs and who knows how many subprocesses.

They are currently discussing how to get on from here, since the framework support will cease within a few years - and the idea of a completely new start (named "The Big Bang" approach) is nothing but scary. Platform migration was done once before - and was entirely cumbersome, resulting in years of patching.

So, the idea is to cut the system up into more or less self-contained parts that may be swapped for specialized new commercial pieces of software.
Main problem now is getting to grips with the connections between software parts, users, and organisational structures. It reminds me of a process I saw with LEGO a few years ago - in which they also were trying to abolish, maintain and develop their software system - all at the same time.

I suddenly thought of visualising the whole thing, when dozing off at a meeting yesterday - so now I am on the lookout for 3D data visualisation tools that may have system data added (preferably along several dimensions) and then show the entirety of the mess. I've looked into a few already on this page - unfortunately, many are quite old...and have no easily accessible interface - which is sort of key - if you want many different actors to use them readily.

Things of note, so far: GraphViz, Atlas info, Tinderbox, mind-mapping.org
The latter points to an interesting list, with 3D Topicscape as the first reference. Promising at first sight - but I quickly found that it was really only a narrowly hierarchical structure that it could visualise. A shame with all that 3D and then they only use it for things better shown on regular diagrams.
I want the x,y,z dimensions to hold parameter references - and nodes that are equally dependent, not necessarily in a parent-child relationship. I want navigation around clouds of connected elements, coloured by their business value, ordered by their program hierarchy, translated by their [insert parameter here].
Still looking....makes me annoyed I didn't become a graphical coder.

[EDIT]
Seems I have found something useful in TheBrain. Not exactly 3D...but the way of adding, linking and dragging nodes has me somewhat persuaded. After all, what good is a big, shiny 3D structure if it is impossible to update easily or navigate quickly. Seems like TopicScape actually imports TheBrain XML-structures...so maybe I can visualise it all more deeply later on.
Next step is to get to work and start adding systems data...=)