For now, Kindle holds the lions share of content for e-readers. Like any large predator however, Kindle has to watch its back. There are any number of competitors that are ready and wiling to take over the throne. If you are unsure, just think about the Barnes and Nobles e-reader. They are more than willing to take over the spot as the top dog. So, that leaves a desktop publisher with a bit of a quandary. Should you just keep formatting for Kindle or target towards a new contender? Of course, before you worry about who to target your formatting to it would be worth finding out if there is even a difference between the formats. After all, there is the possibility that you cold use one document for all e-readers.
As it turns out the formats for the distribution will not be too different. The odds are that if you format conservatively, you can get away with using only one document for multiple readers. You are just going to have to look at some of the hard areas to deal within the formatting. That way you do not have to end up with two versions.
Size Matters
I bet that you always suspected it! Seriously though, you will need to keep your fonts to size 14 and under in order to make the project readable for all readers.
K.I.S.S.
In some places ornate fonts are considered okay. In others that styling fonts can be completely out of the question. That means if you choose to use one of those ornate fonts then you will need to do a second draft with less ornate ones when you do a second copy. Not a fun idea when you have spent hours working on getting the aesthetics just right.
Images
Keep your images high in quality, but low in file size. I know that sounds like an oxymoron, but it can be achieved via the miracle of your image editor. The best way to do this is with your trust image editor. Save at the correct size at a 90% resolution. Do not, I repeat do not compress a larger sized image. Take the time to scale.
As long as you keep within these three basic guidelines you should be fine using the same formatting for submission to multiple readers.