First off, some of the elements aren't aligned properly. Not like what was previously stated with the equidistant stuff, but such as the word "go" on the search button; it looks off a couple pixels to me. Near the footer of the design you have some variations of white and gray background (sorta like a rectangular checker board pattern) - looks like somebody rushed through that and forget to clean up afterwards.
The gradients used for the search bar and footer don't really look to realistic and I think they should be re-worked. The two ads right below the navigation seem to have some out-of-place pixels in the background. The white bar right above the 3 orange boxes looks out of place (its very faint). With the navigation, maybe you could have the little arrow appear when the user hovers over it.
Is that dark gray box going to have some AJAX? If so, that looks like a cool concept. The colors are nice, and the structure is pretty good. However with the 3 boxes near the footer, I think you should make the corners round like every other corner on the design; the right angle clashes with the curves.
Are the ads that you are always going to use have that strong of an orange in it? If not, the comments about the orange being over powering shouldn't apply. I personally think the hue of orange and blue you choose work together very nicely. Also, blue and orange is a pretty common color scheme; we're just use to Sitepoint's color scheme, and their branding has implemented the association of the two into our brain (haha) so don't worry about.
There isn't an equal amount of pixels between the canvas and the edge of the design. If you plan to center the design on the screen, I would fix that. Speaking of positioning take a look at this article:
Designing with a Grid | blog.critical (and you could do a Google to find a lot more). It explains the concept behind keeping your design organized in a grid like format. I think you should make the 3 columns the same width as the square banner, and the 'AJAX' area (gray box that looks like it could be AJAX) the width of 2 columns. This will give you that little detail that makes a design really shine. You'll probably have to expand the size of your design to over 1000 pixels, but it would be worth a shot. Just try not to go over 1024 or you'll lose usability kudos with a ton of users out there.
Also, here is some advice that pertains to the 3 columns. White space = good these days. I think you should get rid of the gray background and make it white. Make the content define itself in the design, not some lines (an example would be the
The New York Times - Breaking News, World News & Multimedia). However I wouldn't get rid of the orange bars. Just try that out maybe and see what you like. I'm a huge fan of simplicity and like many other "Professional Web Designers" have said, its the new way to design.
Some inspiration for the "gray AJAX box" could be gathered from
Yahoo!. As much as some people hate the corporate design style, you can take there ideas and mold them into some visually compelling way (using actual graphics/style haha) that looks bad ass. Yahoo has a bunch of cool AJAX (I think thats what its called) movement kinda things that look really cool. Maybe you could draw some ideas from that.
Overall its not that bad of a design, just a few things can be improved on. Remember, the little details is what makes a design awesome. And with the links that I've provided you; take them as inspiration to get ideas, don't really copy them. However I doubt that has to be mentioned, we aren't at some little-kids-designing-templates forum.
Thats all I can think of for now. I hope you don't feel like I'm bashing your design. I use to be a freelance web designer and I hated it when people commented on my work but didn't really give constructive criticism. I realize that this post isn't really organized that well, sorry about that. I could elaborate a little more, but I really need to study for my last final tomorrow. If you want me to get rid of this post then I will. And trust me, I've seen MUCH worse designs. This one really isn't all that bad, and put that together with your awesome ideas for coding (or at least they sound awesome, I don't know shit about coding) this site is going to whoop some ass! I guess you could call me a perfectionist (easier said than done though, I'm lazy as hell) which explains my nick-picking, long ass post. Hope it helped you out some.