Four years ago, I wrote a RAW converter comparison article called The Mystery of RAW Converters. Here's a one-image update to the article.
RAW converter comparison for underwater sunballs
In the 2004 article, I concluded that I prefer Canon's Digital Photo Professional for RAW conversions when the image contains an underwater sunball. That conclusion still holds.
In general, I find that the Canon 1D series cameras (Mk III, these days) produce "natural", pleasing colors. I almost always like the embedded thumbnail's look more than the thumbnail images that pop up once Aperture or Lightroom generate thumbnails upon import. Aperture tends to boost the image somewhat -- colors are stronger and contrast is higher, but it's not always pleasing when compared to the original.
Underwater photos that contain "the blue" get whacked really badly; photos and distant reef subjects tend to take on a green cast when compared to the colors in JPG images taken straight out of the camera (extracted from RAW files).
Sunballs are still a disaster when images are converted with Aperture or Lightroom. Underwater, I would rather shoot sunball images in JPG mode than use Aperture or Lightroom to convert RAW files -- and believe me, it takes a lot to convince me to shoot JPG over RAW. Luckily, Canon's free software, Digital Photo Professional, continues to do an excellent job in converting underwater sunball images, closely matching the RAW converter built into the camera.