1. Disable the built-in cron module. At least for me, it was hogging the CPU and causing repeated errors that looked like this:

[client 67.210.98.250] script '/var/www/vhosts/default/htdocs/wp-cron.php' not found or unable to stat

You can fix this by commenting out the call to spawn_cron() around line 135 of wp-includes/cron.php.

2. In wp-settings.php, there's use of the HTTP variables $_SERVER['SCRIPT_NAME'] and $_SERVER["REQUEST_URI"] without checking to see if they're defined. My version of Apache doesn't define them, causing errors every time a page was loaded. Again, I commented out the code that makes reference to those variables.

3. The most significant change, the one I described above, is the call to wp_cache_postload() around line 380 of wp-settings.php. Every invocation of this function was taking between five and ten seconds, sometimes more. I believe this is used by WP's built-in object cache, which I wasn't even using. I took out this call and performance went way up.

As I use WP (on a smaller scale) I'd be interested in knowing where the problem was exactly. Have you shared this info on a WordPress forum somewhere?

I spent some time today doing a line-by-line analysis of the code that runs when my site loads, and I think I've pinned down the problem. Ironically, it had to do with a caching module built into WordPress. Just one function was responsible for the vast majority of the time it was taking to load this site's index page. And since my webserver can only hold a limited number of TCP connections open at one time, the problem tends to cascade: a bunch of people connect, and while they're waiting for the index page to load, they're taking up all the available connections for subsequent visitors, who then have to wait in the queue even longer, and so on.

I've removed the call to the misbehaving function, and I think Daylight Atheism is responding a lot better now. Please let me know, readers, if you've observed the same.

Here's hoping it stays fixed.

What I've been noticing is a delay before I start receiving data; after that happens, the page loads in short order.

This is what I've been noticing as well, for the past few (3-5?) days. I'd say it takes 2-3 minutes to connect, then it goes fine. Today, the front page loaded almost instantly (for dial-up), but then it took a minute or two for this page to connect when I wanted to reply to it. IIRC, the status bar says something along the lines of "Waiting for http://www.daylightatheism.org..." (in Firefox 2.0.0.14 on WinXP Pro SP2) for those few minutes.