Though it's trivial to use IkiWiki with nginx you need some tricks to make it work together with the httpauth module and the 404 module.

To make it short, here's a working example (as in "works for me"). The blue lines are required for httpauth while the green lines are required for 404.

location /wiki/ {
    error_page 404 @ikiwiki404;
}

# External reachable ikiwiki.cgi
location /wiki/ikiwiki.cgi {
    # Do basic authentication. Here I pass this task to PAM
    auth_pam              "Admin authentication";
    auth_pam_service_name "nginx";
    fastcgi_param REMOTE_USER $remote_user;

    fastcgi_pass  unix:/var/run/fcgiwrap.socket;
    fastcgi_index ikiwiki.cgi;
    fastcgi_param SCRIPT_FILENAME   /srv/www/htdocs/wiki/ikiwiki.cgi;
    fastcgi_param DOCUMENT_ROOT      /srv/www/htdocs/wiki;

    include /etc/nginx/fastcgi_params;
}

# Another definition for ikiwiki.cgi, only reachable by error_page 404.
location @ikiwiki404 {
    fastcgi_pass  unix:/var/run/fcgiwrap.socket;
    fastcgi_index ikiwiki.cgi;
    fastcgi_param SCRIPT_FILENAME   /srv/www/htdocs/wiki/ikiwiki.cgi;
    fastcgi_param DOCUMENT_ROOT      /srv/www/htdocs/wiki;

    # For 404 plugin
    fastcgi_param QUERY_STRING "";
    fastcgi_param REQUEST_METHOD "get";
    fastcgi_param REDIRECT_STATUS 404;
    fastcgi_param REDIRECT_URL $uri;

    include /etc/nginx/fastcgi_params;
}