I was having a heck of a time calling includes into dynamic archive pages (php files, no extensions). The syntax I used in my Main Index template was NOT working in my dynamic archives. What I found out was that I was using a php shortcut syntax which is not enabled on all servers (and perhaps in my case not in all cases? not sure about that yet - I'll look into an .htaccess solution although I have no reason to believe there is one - just a gut instinct to try)
These worked in the main index, but not in archives:
<? include "http://domain.com/tagline/rotator.php"; ?>
or
<? include "tagline/rotator.php"; ?>
This syntax works in both index AND archives:
<?php include ("http://domain.com/tagline/rotator.php"); ?>
or
<?php include ("links.inc"); ?>
Cool.
Update: having a big "duh!" moment. Forgot about MTInclude as well as plugin MTIncludePlus. The latter provided a solution (new tag MTIncludeURL) for calling includes into my comments.cgi page. (comment listing template,etc) Here's an example of what I used to call a rotating tagline into my banner in dynamic templates that run as cgi:
<MTIncludeURL timeout="15">http://domain.com/tagline/rotator.php</MTIncludeURL>
(obligatory reminder: code is all one line)
NOTE: MTInclude and MTIncludePlus tags slow down the rebuild process. (I only use these tags when a regular php include won't do.) To speed up these tags, consider the MTFastInclude plugin at MTExtensions.