When it's down... ping the website (not the ip). If it's working the DNS is doing it's job.
If it's not working.... you found the problem.
If DNS is ok... then try restarting apache. If this help, great you found the problem. Try checking your logs to see if you have any other problems (dmesg could be a great start). Also check out your load.
If everything is ok, BIND restarted, APACHE restarted and still not working, try pinging the ip. If it's not working, try pinging from
www.dnsstuff.com (do this site your friend).
Check your websites with
www.dnsreport.com, it's a great tool... try resolving all those red marked problems.