Always use the latest version. For the Releases 4.5B and 4.6X, the Note Assistant is updated with the installation package SAP_NOTES. You can download the latest version in the Software Distribution Center in the SAP Service Marketplace.
For the Releases as of SAP Web Application Server 6.10, the Note Assistant is integrated in the standard delivery and is updated with Support Packages for SAP_BASIS. For more information on the latest version (or Support Package level), refer to the SAP Service Marketplace under /noteassistant.