Ems and percents behave differently when a user changes the browser's font size setting (which I think you only see in IE now), but are otherwise the same. Other than that the only advantage is in the fact that ems are a standard convention for designers and typographers, who are used to expressing measurements as a proportion of the text size, and "1 em" is just a more concise representation of that measurement than "100% of the point size of the font in use".