Oh man... Ok, this started out as a frustrated post, but I figured out what was going on... it was just really strange behavior, so if this helps anyone else out there, great.
It’s a standard install, 2.0.0-pl on MAMP with several pages and several templates... one of the templates just wasn’t working. As soon as I would set a page to use that template, not only would the content disappear (despite use of the [[*content]] placeholder), so would vast sections of the template itself. It was strange. So I started putting in search terms into various parts of the template and checking to see if they would show up when the page rendered. They did. But slowly I worked my way towards the center section that was disappearing... and do you know what caused all this trouble?
This:
<ul class="nav-horizontal">
<li><a href="[[~1]]" title="Home">HOME</a></li>
<li>›</li>
<li><a href="[[~11]" title="Map">CONTACT US</a></li>
</ul>
Did you spot it? I forgot a second "]" in my second link. So that template actually rendered like this:
<ul class="nav-horizontal">
<li><a href="index.php?id=1" title="Home">HOME</a></li>
<li>›</li>
<li><a href="index.php?id=11&filter_commands=Array&filter_modifiers=Array
Somehow the missing bracket caused the link placeholder to get interpreted as a filter_commands... and it blew away EVERYTHING in the template down till it found a matching "]" -- the last "]" in the template, which was down by the footer.
The lesson here: if you mess up your placeholders, weird things happen.
☆ A M B ☆