Methods that are intended to be called statically should be defined with static keyword
The $foo =& new Foo() construct should not be used
instanceof operator should be used instead of is_a() function
Declarations of methods in child classes should be compatible with those in parent classes
These changes obviously imply following the Error Handling Guidelines for PHP5 packages since PEAR class itself is not E_STRICT-compatible.
Also the new object model should be taken into account: this means removing unneded references when working with objects and using clone where needed.