Clearing the Pear Cache helps, also in summary:
a) Text_Template has to be uninstalled before Mock_Object which it depends on
b) Token_Stream also has to be uninstalled as version 1.0.1 has to be installed before Code_Coverage which installs 1.1.1 as Scott put it
c) Text_Template has to be installed before Mock_Object which will install the 1.1.1
The final command listing that worked for me is (I am on Windows so I just added sudo before pear for *nix):
sudo pear uninstall phpunit/PHPUnit
sudo pear uninstall phpunit/DbUnit
sudo pear uninstall phpunit/PHP_CodeCoverage
sudo pear uninstall phpunit/File_Iterator
sudo pear uninstall phpunit/PHP_Timer
sudo pear uninstall phpunit/PHPUnit_MockObject
sudo pear uninstall phpunit/Text_Template
sudo pear uninstall phpunit/PHPUnit_Selenium
sudo pear uninstall pear.symfony-project.com/YAML
sudo pear uninstall phpunit/PHP_TokenStream
sudo pear clear-cache
sudo pear install pear.symfony-project.com/YAML-1.0.2
sudo pear install phpunit/PHPUnit_Selenium-1.0.1
sudo pear install phpunit/Text_Template-1.0.0
sudo pear install phpunit/PHPUnit_MockObject-1.0.3
sudo pear install phpunit/PHP_Timer-1.0.0
sudo pear install phpunit/File_Iterator-1.2.3
sudo pear install phpunit/PHP_TokenStream-1.0.1
sudo pear install phpunit/PHP_CodeCoverage-1.0.2
sudo pear install phpunit/DbUnit-1.0.0
sudo pear install phpunit/PHPUnit-3.5.15
