Yeah, back in my defense-contractor days we built several video walls for connected C&C rooms.
The high-end systems could put multi-display graphics at 1080p60 from any console to the theater and were based around the 64x64 Thinklogical DCS KVM over fiber modems and fed into a VistaSystems Spyder 12x8 video wall controller (of course they have larger units to drive your 3x3 wall, and you'd also be able to have a "preview" scaled down display of the entire wall which is also good for recording or broadcast). This pretty much lets you juggle sources around your video wall like in Minority Report. Good for theater events and presentations, maybe overkill for a 24x7 control room. The advantage was that you could plug literally anything anywhere and compose it on to the video wall somewhere.
Lower-cost systems were built around RGB Spectrum Quadview - type video wall controllers. These weren't as smooth and glitzy, but could get the bits displayed. The main benefit over software systems is you could zoom in and fill the entire wall with one important display, and you wouldn't have silly screen synchronization issues, which are quite noticeable and distracting (particularly when you put on a movie or sports event)
The point is to use the video wall as a cohesive display and not a matrix of disconnected monitors. It sounds like you're trying to build the latter, though. Personally I haven't found any of those types of displays to be very useful to the actual operators in the NOC, they have their own workstations showing everything they need, so I would say the main purpose of such a wall should be the ability to grab a few displays of any of the NOC operators and post them on the wall to allow them to communicate what they see to observers. But since the NOC operators are busy fighting fires, you'd want a separate AV controller station who can pick out the displays that are useful and freeze and post them to the video wall, be able to screenshot and rewind the video feeds to show notable events, reconstruct a timeline of events, etc.
It's possible to cobble something like this on the cheap using VNC (as long as audio and full motion 3D / video are critical) using vncproxy, vncrecorder, xosd (labeling sources is pretty important), and a few other things. This sounds the most like what you're trying to do, but seems like kind of a waste for the central 3x3 matrix wall. Be sure to use one of the "tight encoding" variants of VNC, such as tightvnc, tigervnc, or ultravnc on Win32, since the screenscraping performance really improves latency and frame rate (not enough for FMV, but close). With your thin client solution, you might be able to hack something together using VLC to each display a different part of a movie, but synchronization will be a big issue.
In short, you probably want a video wall solution + matrix switcher to get the full frame rate and all the bits from any source, and plug any half-assed software compositing solution into that. That's the better approach If you want to get any bit of your money's worth out of the big expensive LCD wall.