I'm going to chime in and say that I will dearly miss the magazine layout, as it was one of the most distinctive setups I have ever encountered, and I really enjoyed it. BUT, with the addition of the ToC at the bottom of each article, many of my initial concerns are taken care of (I thought about posting yesterday, when this first happened, and refrained because I wouldn't've been nearly as friendly).
//begin rant
The only thing left that I really find jarring is the placement of the tags. They're jumbled, and everywhere, and mostly look like *self-censured*. I appreciate that you've got a tagging system, and you want to make it accessible, but everywhere I look I see:
Excellent, Evocative Title
By Author
fanboy, horse, peanut butter, puppies, Queen Elizabeth, socks
The site was always so clean and slick before. The tag placement just doesn't look good. Additionally, if I'm reading an article, aren't tags the last thing I'm interested in? They're maybe how I got there, but I don't think most (non-ADD) people arrive at an article, go, "Flower Power", "By Spanner", oooooo "pokemon". I read the article, I enjoy the article, and THEN I become interested in where else the wonderful web2.0 might lead.
//end rant
In the end, it will take more than a format change to keep me from coming back, as the content is some of the best out there. Thank you for trying to address the initial concerns so quickly, you guys are all awesome.
edit: P.S. I just noticed that in the "What's new" and everywhere else with Comment links, its no longer possible to jump directly to the most recent comment. Maybe this was a glitch that I enjoyed exploiting previously, but it was nice, if I'd been following a particular thread closely, to hit the homepage, see that people had responded, and jump directly to the most recent comment. Still not a deal-breaker.
edit^2: Latest Post links are now working! W00T! Or maybe they were working before, and my browser was just malfunctioning.