What is the ideal setup to address security concerns?

I’m aware of the requirements WP has for certain directories and files to be writable. I’m also aware that making permissions too loose can open security holes. Finally, I know that the user that (insert your server here) runs as on Linux systems can be a factor.

Security aside, I like being able to download themes and plugins to my blog, and update them when necessary. Proper permissions seem to be a bit at odds with this preference.

I’ve collected little bits of detail here and there, but I’d like to see a more definitive answer, if there is one: what is the preferred setup with a nod to security? What permissions should be in place, what user should the site run as, etc.

If you have FTP access to your server, the most secure setup is not having your themes or plugins directory writable by your webserver and instead having WordPress update files using FTP. When you go to update a plugin, WordPress will prompt you for your FTP details.

The FTP method is a lot slower than direct file writes, but it is a lot more secure as a rogue script won’t be able to modify your files.