There’s no set best practice, as each model fits different work processes.

One Repository

If you’re only managing a single site with a single set of plugins/themes then a single repository makes sense. Or if you’re managing multiple sites that use the same set of plugins/themes.

Multiple Repositories

_{This is my personal preference.}

Keep WordPress core under SVN version control so it tracks the official repository. Then check out/clone each plugin or theme as needed separately.

I often clone all of my plugins via Git to a special folder on my machine, then symlink each to folders in /wp-content. Not the prettiest way to do it, but I can use one local copy of a plugin in multiple, independent test installations of WordPress.