For most purchasers, the Professional Edition is the appropriate choice.
The Professional Edition supports all standard protocols such as FTP, FTPS, SFTP, SCP, HTTP & HTTPS. It supports Windows domain users, event notifications and process triggers, quotas, SSH terminal access and advanced file permissions.
The Standard Edition is for those who want the minimum features of FTP, FTPS and SFTP for the lowest possible price.
The Enterprise Edition should be considered by those who want to add custom functionality of their own to CompleteFTP, or who need multiple sites supported on the one server. The Enterprise Edition also now has the multi-protocol gateway for adding secure access to other servers, or for protocol translation.
A feature comparison can be found here.