Here are my suggestions:

You have a lot of wasted space in the upper-right corner. Move the Subsribe and [/i]Podcast[/i] links down to the navigation bar, directly beneath their current location. Now, move the topmost ad to the newly-created extra space to the right of your logo (you may have to make your logo slightly smaller).

The story text is too spacious. Try compacting it a little.

Right now, you have two sidebars ...having only one would look much better. I would get rid of one of the ads (if possible), and have everything else in one single sidebar, in this order, from top to bottom:
-The History Channel, Universe ad
-Google Search (needs a little work, see below*)
-Email signup
-Large Google Ad
-Calendar
-Categories
-Other ad
-Blogroll (P.S. fit "The Skeptics Guide to the Universe" onto one line - or link to the "NESS" instead)
-Google Adsense Badge (possibly move to the bottom-right corner)

* - The Google Search is slightly too wide. Perhaps make the "new" sidebar a little wider.

Also, the page is a bit long. If the new, single sidebar doesn't already go to the bottom of the page, consider putting a few less stories per page.

Of course, I'm not sure if all of these suggestions are realistic or even feasible, and as always, it's your site, so you can do whatever you want.

EDIT: After re-reading your post above, it seems that you may have already tried a single column design. (Unfortunately I can't remember what the past site looked like). ...Have you considered adding one of the ads along the side, to the bottom (horizontally) instead? ...That may lead to a little less clutter, and maybe even free up enough space to place everything in one column.