This video show the effect in action. It's a very simple scene and render. Made with blender 2.5 beta 2.

The principle is really simple :

1. Make a full step animation of something like if there's not matrix effect. Well assume your animation have 500 frames of physics.
2. Then you can create a camera, position it, make some move target the focused object (for instance).
3. You render 250 frame of the object moving to the target.
4. You save the blend file to TEMP.blend.
5. You open another blender and load that TEMP.blend
6. You delete all IPO curve of the physics of the object. (Take care to be at frame 250). After that you'll have normally a model that should be still.
7. You delete IPO curve of the camera as well (The camera should stay at the original location of the 250th frame).
8. Then you make a new IPO curve for the camera focusing the target and moving around for about 100 frame (for exemple).
9. Render it. (You've now 2 part of video).
10. Then take note of the last position and rotation of the "turning around" camera you've just played before in the 100th frame of the Matrix effect.
11. After you can close that blender session and came back to the old one.
12. Now you are in the old blender in the 250th frame, simply paste position & rotation of the camera in the right panel (screenshot).
13. Clear IPO for the cam and make new IPO if needed then render then last 250 frames.
14. Et voila, normally you should have 3 part of video that you'll just have to append to obtain a similar of temporal matrix effect.

That's how I do for that video. There's way to lost less time but it's sufficient for now :)

Another good idea, whould be to make a time distortion to slow down the physics while keeping the camera moving at the real rate... But I don't know blender IPO curves as well as to manipulate all ipo curves of each object included in the physics :D