Over all, this design is an improvement over the last one, from a sheer concept standpoint, but there are still remaining issues.
The color of the logo is okay. It's eye-catching without being too bright on its own; however while I like the concept of the logo, I am not sold on this version. It certainly looks more like a person now, but with the tilt of its head and the angle of its torso, it looks very sad. Perhaps if there were a something like a hand in front (ala The Thinker), it would have a different feel. You mentioned that you had several versions in the works. Any chance that we could see some of the others?
I like that "skeptics" is written in lowercase. It separates us from the conspiracy nuts, and feels inviting.
The concept for the background is great. I like that it contains scientific papers, and that they are muted so as to not compete with the content. It works as a concept, although it seems a bit dull. Is it possible to have several different backgrounds in a similar style that can be cycled through? If we have to look at that same graph all the time, it seems like it would get tiresome. Also, I don't know if it is just a matter of the preview image or not, but the background suffers from JPEG artifacts pretty bad. I assume that that is just a matter of the preview image, but if not then that should be changed.
I like that the color palette is restricted, but I don't know if the yellow and lime green are the best choices. The color at the top of the page works well enough. The yellow appears to be more muted here than the rest of the page. It contrasts well with the darker gray of the background; however when this is reversed on the bottom of the page, it becomes difficult to read the text against the yellow. I generally do not like the way that the yellow is used throughout the site. It's a very attention-grabbing color, and seeing it on Xs, numbers, quote lines, and as the background for the author info box is very jarring, as they are less important to me than other areas of the site. I would reserve it for VERY rare cases, and places where it is vitally important to draw the attention of the user.
The green on the white doesn't have enough contrast. It should either be darker or more saturated to make it more visible. It basically looks like the questions with answers are less important than the ones without.
Helvetica and Verdana are good choices.
The icons are clear, and look like buttons. I just don't like the yellow in the activated states.
The only issue that I have with the merchandise is related to the logo. I love the last shirt.