OK, some quick comments, in order as I explore the site...
The site looks a bit odd stuck in the upper left corner of the viewport. Have you considered centering it, at least horizontally?
What is the point of those icons on the portfolio page? If they were thumbnails, I could understand that, but essentially they are just bullets--and they seem way too large for just bullets. Also, it would make more sense to me to click on the actual text rather than the bullets. If it were me, I would just get rid of the bullets entirely. At the very least, you should make the portfolio page titles clickable (links).
There seems to be some overlap between the writings page and the blog page, in particular the post entitled "Grimwell Online is back!" That would strike me as something that belonged on the blog page rather than the writings page. Same goes for the next post ("Typical Spring"). You might want to pick a word limit for posts--anything under the limit goes into the blog, anything over the limit goes into writings.
Having some more information in the archives would be helpful--namely, where each of the posts comes from (blog, writings, etc.).
After taking a look through the whole site (with the exception of the portfolio pages), two thoughts come to mind:
1) The home page isn't really the best start page, I don't think. In fact, I don't really think it's necessary at all. It's filler and nothing more. Why not just make the blog the main page? I know you said above that you don't want it to "just look like a blog," but I don't really see how adding a pointless start page helps. I would scrap the home page or make it more useful.
2) I'm wondering about the distinction between the writings page and the blog--is it really needed? Why not just have a single page called "writings" and keep both your long and short writings there? I got this impression when I first looked at the writings and blog pages, and it was reinforced when I finally got to the sections on the right hand side. Having this section menu makes the distinction between writings and blog fairly meaningless, because people can get directly to the type of posts they want to see anyway.
Although I'm not familiar with what your site was like before the redesign, I'm guessing that these two things are the result of your attempt to move away from a "just a blog" site. But I can tell you that, while these changes may make sense to you, they don't make much sense to someone coming to your site for the first time (or at least to me). Being "just a blog" is about content, not presentation and structure. If you have more than blog content on your site, your site will be more than a blog. If you only have blog content on your site, no amount of finagling is ever going to make it more than a blog. In short: don't try to impose artificial divisions on the site to make it seem less blog-like, just let the content speak for itself.
Needless to say, these are just my opinions.
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Suho: www.liminality.org | Cell 270 | Sig Rotator | the Fellowship of Sup