I'm almost done writing my book EPUB Straight to the Point: Creating ebooks for the Apple iPad and other ereaders. I've been writing it in Adobe InDesign CS5, and typically when I finish a book, I convert all my illustrations from RGB to CMYK before sending the files on to the printer. Without going into the whys and wherefores of RGB vs CMYK, screen vs print, etc., etc., you should know that the CMYK versions of originally-RGB images tend to be slightly darker and more muted. You simply cannot create the same colors on paper as you can on screen.
For this book, I'm creating both a print and an EPUB version of my book (following the instructions in the book itself!) And it occurred to me that the EPUB version of my book is destined for RGB screens like the iPad, and so I want to use the RGB images in the EPUB—not the CMYK.
Here, for example, is the original RGB version of one of the screenshots in my book:
Notice particularly how vivid the red arrows are, and how bright the green W is at the beginning of the page.
Now here is the CMYK version destined for print:
In the converted CMYK version, the red arrows are much darker and the bright green W is much more muted.
The solution is to export to EPUB before converting your images to CMYK.
If you make changes to the content later and need to reexport the EPUB file, as long as you haven't changed the images, you can just copy the images folder from the older EPUB to the newer one. At least that's my plan. I'll let you know how it goes.