Um, it didn't turn out as expected. (It's not bad but... It's not super-great either)
http://www.youtube.com/watch?v=Ope1Y0cmTsQ
I used this in Avisynth:
Lanczos4Resize(960, 720, 0, 0.5) # Lanczos4 (Neutral)
ConvertToYV12()
Why did this not end up as clear as yours did?
It's hard to say, but color-wise you might need to need to specify a color matrix. The default is REC601, which is wrong for a PC recording (definitely so for Fraps, should be the same for Hypercam) and uses TV levels (16-235) instead of PC levels (0-255). I've used both Fraps recording directly to YV12 and Fraps in RGB mode (see
this).
This is my paranoid x264 profile (goes in 'MeGUI\allprofiles\x264'). The UFO Stage 6 video was encoded with CRF20 instead of CRF16 as a test.
EDIT: Also, it looks a little choppy. I'm not sure if that's how my machine is handling it so...
Take a look at this screenshot at full size:

Notice how the bullets have a translucent "clone" in front of them? I've been testing blending the two frames instead of dropping them, which creates a smoother video than how Youtube handles the conversion. That "clone" is the bullet in the next frame of the video at 60 FPS, which would be outright removed by Youtube.
I did notice on Murasa's bullets that the fast ones didn't retain their shape very well, so I may have to experiment with weaker settings so the bullet's...before-image (or whatever) is more transparent. Overall it makes the videos look nicer in motion.
The script looks something like this:
function BlendFields(clip) {
clip
(FrameCount % 2 == 1) ? DuplicateFrame(FrameCount - 1) : nop
Overlay(SelectEven, SelectOdd, opacity=0.5)
}
clip1 = DirectShowSource("Z:\Fraps_Videos\th12 2011-03-09 16-13-41-86.avi", fps=60)
clip2 = DirectShowSource("Z:\Fraps_Videos\th12 2011-03-09 16-15-47-08.avi", fps=60)
clip3 = DirectShowSource("Z:\Fraps_Videos\th12 2011-03-09 16-17-52-32.avi", fps=60)
clip4 = DirectShowSource("Z:\Fraps_Videos\th12 2011-03-09 16-19-52-95.avi", fps=60)
clip1 ++ clip2 ++ clip3 ++ clip4
Lanczos4Resize(960, 720)
BlendFields
trim(2963, 2963 + 9094)
AddBorders(160, 0, 160, 0, 0)
ConvertToYV12(matrix="PC.709", interlaced=false)
The call to BlendFields should be before any trim calls (it also reduces the frame rate to 30), and after you resize the video.