We recommend rooting Web server content in /web (typically a symlink to a large mirrored disk drive). Since most servers these days are expected to run multiple services from multiple IP addresses, each server gets a subdirectory from /web. For example, http://scorecard.org would be rooted at /web/scorecard on one of our machines and if http://jobdirect.com were on the same box then it would be at /web/jobdirect.
For the sake of argument, we're going to assume that your service is called "yourdomain", is going to be at http://yourdomain.com and is rooted at /web/yourdomain in the Unix file system. Note that you'll find our definitions files starting out with "yourdomain.com".