Apparently, PEAR.php got left out of the latest ebuild of php. After I installed PEAR-DB and tried to use a web app (drupal) that uses PEAR-DB, I got an include error saying that PEAR.php couldn't be found on the include path. According to slocate, PEAR.php wasn't anywhere on my system.
I suspect you don't have xml AND xml2 in your USE flags. PHP needs both of them in there when it builds to include PEAR.
Fixed in CVS. Please test.
closing old bugs.