A couple of points / whining:

• On the main page, it is not clear whether the up/down/save/hide icons belong to the post above or below it. I would suggest removing the line above these links.
• I would like a link to the article or to the comments at the bottom of the article, but I suppose this has been mentioned already.
• Give me back my text links instead of icons, I liked the simple look it gave the side, and it is easier to understand. The vote up/down buttons are easy enough to understand, but the other icons are not. When I want the permalink, I don't immediately know what to look for. Also, the pop-up balloons are annoying, and would be unnecessary if text links were used.
• Also, it is not immediately obvious if an up/down vote icon has been clicked. It turns green, but there is already lots of green on the page.
• Why are the text input fields in ugly blurry gray? I would prefer a crisp edge.
• Why is the text of buttons gray on a gray background? I would suggest using black text for a better contrast.
• The green border for new comments is a bit much. I would prefer it if it just said "new" somewhere. Or with an icon if you are so inclined.