Few things come to my mind and what i would do.
Remove that huge belt buckle surrounding Simple Geek and that grey background from top right nav. Let it just sit on the canvas. Remove radius and box shadow from article and add bottom shadow. I like that textured background.
That gray color in article header does not match at all the bluish background. Try this matching color instead #7192A8 with off white text.
Increase left and right padding in your section to at least 20px.
Looking better. When you redo the logo keep in mind “simple”. I would also redesign the nav buttons and make them a one solid color.
Also, the drop shadow on the search box does not match the rest of the site.
Keep working at it, you will get there.
I didn’t see the site with the gradients everyone mentioned. What I see now I really like. Very nice background texture, and the soft blue color scheme is relaxing and professional looking.
I agree with springlab, that when you redo the logo, keep it clean and simple. Ditto to his suggestion about the nav buttons. I find that the site looks soothing and very attractive, but the logo looks out of place, breaking the overall harmonious mood. As do the nav buttons, but to a lesser extent.
I fixed up the search box. My thinking was to make it stand out just a bit with the original shading and corner radius.
As far as the nav buttons. I wanted to do something a bit different, but it is obvious that they don’t really fit now with the changes. Which leaves the question of what to do? I could do a nav bar with sprites next to the button text with a very subtle gradient or no gradient. It seems that I went way overboard, or gradients are out of style for most anything but buttons.
Logo definitely needs work. While I love the shiny plastic blue look, it does not fit anymore.