Wall of text alert! Also, I have too many opinions for my own good : )
Beta 2 is a great improvement over Beta 1, but I agree that there is some work to be done still. The most recent mockup above would be a good layout. Part of what I think Tom's needs to consider is the screen resolution. If they're keeping the width optimized for 1024*768, the height should be as well. Having a banner ad under the searchbox - like there has been on all of the iterations so far - really cuts into the 768 pixels of vertical space. For those of us who spend a lot of time doing web browsing on computers with 768 or 800 px of vertical space, that's what really counts. The current layout allows me to see 3 articles and 12-16 news stories from the top of the home page in 768px of height (not counting the browser window and the XP taskbar). Beta 1 actually let me see more news and articles, but if I scrolled down I wanted to stab myself in the eyeball. With Beta 2, I can see at most 6 stories, but 6 articles at my fingertips. That's not really balanced compared to the pace that the two sections move at.
Now, the only improvement I see having been made to the original homepage was in the top <768 pixels of Beta 1. What I'd change about that is to remove the banner ad, and put the forum feed in where featured topics was - and move the 'ask a question' button to the top. Alternatively, the original layout could remain, with some consolidation of the stuff down below, and the forum feed could be where 'topics' and the square ad is - keeping the banner ad at the top, and pushing the square ad down.
Although the overall impression of Beta 2 is better, the first impression of Beta 1 is cleaner. The current default combines the best of both, but is missing the forum feed.