I'm wondering if set widths and heights in em could be help ?
No, if something's set in em's and that's wider than the width of the mobile's screen, you've got a problem... scrolling sideways. That's what you're avoiding. You leave things to a fluid width. You don't have boxes side-by-side: for mobile boxes will sit on top of each other.
So for the aside section I can only use absolute positioning ?
No, you'll save any positioning for the Desktops wide enough to fit two things side by side. No sidebars. Sure, an iPad is likely wide enough for something and a sidebar, but what about a mobile with 100px of width? (heck I can't even make a site that works at that size just because my form controls are wider than 100px sometimes... can't change that either)
What about embedding videos and it's worth
develop a html5 layout at least for the mobile ?
I don't know anything about video, however I'm guessing you're thinking of the iWhatevers and their lack of Flash support and hoping the <video> tag will help you.
Since there are all those other user agents who don't support HTML5 and don't support <video>, you'll be using Flash anyway, at least as a backup (set the Flash file inside the <video> tag after the video data... You can have <object> tags inside <video> tags, since <video> tags allow you to list alternatives inside... browsers who don't support <video> should just see the <object> tag with the Flash in it like normal... browsers who support <video> will try to grab the file you have listed first in the <video> tag).
You could use the HTML5 doctype (<!doctype html>) and just video tags (using the graceful degradation technique I mentioned above for all the non-brand-new browsers out there like IE8) and be okay. Mobiles aren't any better with HTML5 as a group than anyone else, and I'll still argue that since the iWhatevers are very low % worldwide and that feature phones and "lower" still strongly outnumber smart phones with uber-modern browsers, I would not expect HTML5 in and of itself to be a huge benefit, just <video> for the iWhatevers.