Canon Color Matrix vs. Histogram

The following chart illustrates the effects that changing the color mode has on the histogram of a static subject.
The subject was a row of various neon-colored bathroom cleaner containers, and with some deep black ink, lit by tungstun room lighting.
The camera was a Canon 1Ds, in manual mode, set to JPG large/fine, with zero sharpening.

It has been suggested that the JPG settings are applied to the thumbnail which is shown on the camera's review LCD, and that the histogram is then calculated from this thumbnail.

This effect is important to RAW image shooters who desire to expose as 'far right' / as bright a scene as possible, to avoid image noise, and without overexposing the highlights.

The five graph lines / color modes are as follows:
1 - natural-looking hue and chroma
2 - hue and chroma suitable for portraits
3 - hue and chroma similar to high-chroma slide film
4 - Adobe RGB
5 - low chroma (my understanding is that this is the camera's native color space)

DEEP SHADOWS  (the far left verticle line)
Option 3 puts a considerable number of pixels in the deep shadows, followed by 1, 2, 5 and 4 with the least.

MID-SHADOWS  (the first upward slope and peak)
High-chroma option 3 darkens this area the most, while Adobe RGB is the brightest.  Portrait-mode # 2 creates a peak considerably to the upper right of the other options.

MID-TONES  (the next two peaks)
The high-chroma option 3 peaks higher and more to the right in the darker mid-tone peak, while the portrait mode #2 is shifted to the bright side.

UPPER MID-TONES / LOWER HIGHLIGHTS  (the last peak, and downslope)
This is the important part for those who shoot high-contrast scenes.  Low-chroma option # 1 is the darkest (thereby giving the most headroom to avoid blown highlights), with Adobe RGB mostly overlaid, while the remaining three color options are considerably brighter.

CONCLUSION
If you are having trouble with noise in the shadows, and blown out highlights, shoot in color mode 4 or 5.  If you are shooting under controlled lighting, or need to retain / enhance fine gradations in hue, use one of the other 3 options.