The Portable PHP password hashing framework allows advanced password hashing offering increased security over simple MD5- or SHA1-hashed passwords. phpass is already in use in some larger projects such as WordPress (since v2.5), Drupal 7 and phpBB 3.
Authentication and Authorization is a good tutorial. Among other topics, it describes basic aspects of Yii's RBAC implementation. But however hard I read the tutorial, I couldn't understand how exactly the hierarchy works. I found how to define authorization hierarchy, how business rules are evaluated, how to configure authManager, but almost nothing about how I should build my hierarchy, in what sequence its nodes are checked, when the checking process stops and what would be the checking result.
Yii's by-default directory organization works well enough, but there are several steps one can take that improve the security and serviceability of the system, especially in the context of multiple Yii projects on the same machine (including multiple versions of the same project).