I would strongly recommend not to use "em" units for margins or paddings. If you want "flexible" units, it's better to use "%". "em" units are relative to the font size of the parent element; also, they are affected by the font size specified in the user's browser. "%" units are relative to size of the parent element and are not affected by the font size specified in the user's browser.
Take a look at these samples (in all of them, the blue line shows the alignment on those elements whose margin was defined in "%" units, the green line is for those whose margin was defined in "em" units):
IE7 and font sizes set in browser were medium, larger, and largest
Firefox 3. (in browser) Font sizes were set to 16, 20, 26
Opera 9.27. (in browser) Font sizes were set to 16, 21, 26
Safari 6. (in browser) Font sizes were set to 16, 21, 26
In all the examples, I'm using two fonts: Arial and Times New
The test page can be found here
Just imagine, defining margins/padding in "em" units can produce undesired results in a layout if a user has set, in their browser, a font size different to the default one (which usually is 16).
Even though "zooming" would preserve the layout if margins/paddings are define in "em" units, it's always of good practice to keep in mind those users who would set a font size bigger than 16 just so they don't have to "zoom in" every time they read a blog/site whose font is too small for them.