nginx.conf

limit_zone conn_from_one_ip $binary_remote_addr 16m;
limit_req_zone $binary_remote_addr zone=lreq:20m rate=2r/s;
proxy_cache_path /usr/local/etc/nginx/cache levels=1:2 keys_zone=one:16$
proxy_temp_path /usr/local/etc/nginx/temp;

...

include sites/* ;
}

server {
listen 80;
server_name site1 ip1;
proxy_temp_path /usr/local/etc/nginx/site1;
limit_conn conn_from_one_ip 49;

server {
listen 80;
server_name site2 ip3;
proxy_temp_path /usr/local/etc/nginx/site2;
limit_conn conn_from_one_ip 49;

И вот так из 6ти хостов, работает только на 3х