variable_set() should be called only when needed.

This little line causes a server under load to start falling over... http://nathan.rambeck.org/blog/19-drupal-performance-and-variable-cache
variable_set('include_set_root', $done = TRUE);

That particular line occurs within the include_set_root() function, which gets called (at most) once per non-cached page request. If you bother to read the code, you'll notice that variable_set() is only called if variable_get() returns FALSE.

In other words, the variable is set (at most) once per Drupal installation, unless you uninstall and reinstall the include module. If setting a single persistent variable exactly once causes your server to fall over, you need to get a new server.

Closing this issue. If you still believe that using the Drupal API constitutes an "epic performance fail", I suggest that you start writing your web applications in C or C++.

Okay, I re-read my own code and see that variable_set is being called in the wrong place. Mea culpa; I'm now eating crow.

(fixing...)

Changed in git; will roll new release shortly.

Fixed in 6.x-1.8 release.