pear uninstall [options] [channel/]<package>
So if you wanted to uninstall PHPUnit
pear uninstall phpunit/PHPUnit
Note: remember to preface with sudo or you won't have permission to uninstall anything.
sudo
pear uninstall package_name
You can read about it here in the PHP Cookbook
If you're on a RPM Linux Distro, it's simple with YUM
If you installed a PEAR package with YUM you can uninstall with YUM as well.
yum install php-pear-db
to install and
yum remove php-pear-db
to remove.