It's pretty rare that I encounter a bug in the software I run that hampers my ability to work or my server environment's ability to function normally. However, I encountered one last week that has taken me and several Rackspace support technicians nearly a week to figure out, namely PHP bug #43677.
The issue was that PHP seemed to be "forgetting" the include_path in the current script (not Apache). The bug has been found in PHP 5.2.5 (and possible in all of the 5.2.x releases as well). The problem has been fixed in the latest CVS version and a patch has been created for those that want to correct the problem right away.