Alright, so I'm still very interested in what the GC & Wii offer in terms of video output and what we can do with them. I've found a few things and thought I would post some of it for the few others out there also interested (and so maybe we could help each other out!).
I was right about RGB existing natively in the cube (which makes sense since YCbCr is actually derived from it), however I was unfortunately wrong about just popping off the case and having at it. The colorspace conversion is done within the GPU (the "Flipper" chip), inaccessible* to us. The data then goes to a different chip on the motherboard, the video encoder (U6 on the underside of the board) as YCbCr. The data bus that transfers this is actually what the digital video port (on the earlier cube models) links into, conveniently preceding pretty much all of the standard conversions! A nice offer by Nintendo, even if it was short-lived. And this means that it doesn't matter if you don't have that fancy digital output port; any GameCube can still be hooked up with component cables (which yield a much better picture).
Another thing: The video encoder (digital to analog converter - DAC) is what converts the digital YCbCr to the various analog outputs (depending on the system's region), offered via the standard A/V plug on the back of the system. A different chip isn't used for each region. The chip can actually operate in different modes to produce either Composite and S-Video (for NTSC) or Composite and RGB (for PAL).** The mode is selected by part of the digital video input (during the blanking period the CbCr lines give timing information). Tracing that back to the GPU, that mode select is determined by registers, which are, I assume, essentially the GameCube's OS registry. This makes a lot of sense because it means the hardware can all be the same from region to region, making the system easier to produce. I haven't done a whole lot of searching on how to change these registers yet. But it would be neat to have a NTSC cube output RGB. You could use that for VGA and a standard computer monitor. I'm betting it's much easier on the Wii since there's so much out there on softmodding.
*Before going to be converted to YCbCr, the RGB video is buffered into the main memory chips on the board (the two "MoSys" chips, U3/U4, above the Flipper). So theoretically you could access this since it's external to the chip. But I'm not really sure how this happens (i.e. what pins, serial/parallel, etc.), so I'm not sure how one would tap into this. Also, the interface that then accesses and converts this to YCbCr I think does other adjustments such as setting the resolution (also configurable by registers btw) and cropping.
**It can actually run in 4 different modes: NTSC, PAL, M-PAL, and debug.