I hate that I have to manually (or scriptedly) call cron.php for every Drupal site I run. Even for multiple Drupal sites on the same server in a multisite configuration. Yes, there are ways to automate it, but eventually they fail. I just manually called cron.php on one of our main sites, after realizing it had silently failed for the last 32 weeks. Hundreds of reminder emails are being sent out now, for events that were held months ago. Yes, there are modules to have cron.php called periodically (poor man's cron...) but they're flakey at best, and risky at worst (there is a chance of overlapping cron.php calls if the timing is just right).
Anyway, there endeth the rant. D'Arcy's Drupal Pet Peeve #1: cron.php