The NSA has published their Guide to the Secure Configuration of Red Hat Enterprise Linux 5. This is an excellent document that describes best practices for securing a Linux system – tailored to Red Hat Enterprise Linux 5. It starts with best practices, such as, encrypt transmitted data and minimize installed software. It then follows up with exact configuration recommendations, for example, the exact configuration option to prevent root from logging in directly via ssh (Section 22.214.171.124). They do a pretty good job describing the rationale for making the changes that they recommend (“The root user should never be allowed to login directly over a network, as this both reduces auditable information about who ran privileged commands on the system and allows direct attack attempts on root’s password.”). If you are responsible for the security of any Linux system (whether as a developer or an administrator), I highly recommend taking a look at this document and thinking twice about any decision that you make that runs counter to these recommendations.
EDIT 4/21/2009: updated a corruption that rendered the ‘ in the word root’s incorrect
The new location for the guide is http://www.nsa.gov/ia/_files/os/redhat/rhel5-guide-i731.pdf