This is not an official re-design of FA, but I just decided to have a crack at it as I feel that even as it is right now, it wouldn't take much work to make the site more visually attractive.
I designed it attempting to use only what FA currently has to offer (except for a few text suggestions, but those were just added for my own pleasure).

for a clearer and slightly larger version of the image, see here.

I'm gonna add my answers to some comments here so i dont have to answer them twice XD

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I'd put the comments either side of the banner
i had them there, and it looked horrible. Too much happening along one line. it's very bad practice to put your website name in the same line as unrelated advertisements. If you have too many different images along one horizontal line (especially ads that flicker), your eye finds it hard to focus, you'll keep glacing back and forth.

Good designing practice it to put all the same elements together, and not to mix unrelated objects (eg header and ads). Putting different objects along the same line gives the impression they are of equal value, or equal content. You'll notice in magazines and newspapers that the more important things get more visual real estate than the lesser ones, and they split them into a hierarchy (aka not side by side, unless you're dealing in columns, in which case the hierarchy is set separately for each column.

As this website is for the most part a single column site, it's important to maintain a hierarchy visually to direct the viewers attention from one thing to another.

Another reason for not having ads at the side is that the website has a fluid width. This mean the site stretches to the size of the browser, and thus, having ads on the sides would break when viewed on a small sized browser window or a mobile device, making the site look even worse from the browser attempting to re-align things, or making you scroll horizontally when you shouldn't need to, or scaling the website down to fit and making the site un-readable.

The Banner is too big
I gave the banner a bigger space and it's on area to command attention, and then the ads underneath as they are secondary but still important.
Now, it might be too big, but I reckon it deserves much more room than it has now. Some banners are beautifully designed and you loose a lot of it one it gets shrunk down.

If you're gonna let people make pretty banners, them give 'em a decent space to show it off! XD
Otherwise you might as well do what DA has done, and just make a tiny icon in the top somewhere that no-one notices.

Who made the Banner?
Here they are: http://www.furaffinity.net/view/5117280/