In our system-administration tasks with Drupal, my team found a couple of issues related to how Drupal handles files that other users might find useful to know about. I do not have workarounds.

We found with both Drupal and our Java app server that symlinking the base installation directory can cause problems. When I installed Drupal in /var/www.drupal-6.8 but pointed Apache to symlink /var/www/drupal, I got intermittent white screens. The Java server was similar, it resolves to real paths in its auto-generated configurations and that caused us problems during upgrades.