It's true that pixels are easier to align, or even measure in general. But for text, I think, it's better to use em's. My boss has a bad vision, so every time I demonstrate him something, he wants to put the text size bigger. If your text has a fixed pixel-height, he can't do that.
That's why I always end up with putting the text in em's, and avoiding fixed height elements (divs). Once max-height & max-width are fully supported in IE, you can make sure your layout still looks good, while using em's.