After trying to make sense of "Hackers" representation of the cyberspace, I came up with something I call "Machine Room Metaphor".
Consider the following:
Processes running in the system are represented by arbitrary sized boxes.
User can move and manipulate them to his liking, but by default they are stacked on top of each other as if they were rack mounted servers in a data center.
Every box has a front panel and I/O panel.
By default, front panel displays process' name but process can change it to display image data and recieve events from user interaction (text input, virtual cursor, "touch", maybe something else). This can be used to emulate traditional virtual monitor or just a collection of buttons, levers and indicators.
I/O panel hosts series of connectors, through which User can attach running processes to each other via virtual cables.
"Portals"/"Doors" connect different "machine rooms" which can be on different servers in the network or concurently running on single computer, and cables can run through them (having the ability to carry processes around would be cool too).
You don't even need a VR helmet for this, it would somewhat work on a standard screen+mouse+keyboard combo with familiar shootery controls.