Only do it if you have 2 dedicated servers and you want to test them. If you have a site on a shared server and run that it will affect all 500 other sites on the server and the hosting company will complain to your ISP or shut your web site down if you're running it from another shared server because port scanning is against the TOS of most hosts (and ISPs)... which won't be fun for you.
[quote author=bargainbloodhound link=topic=2794.msg10015#msg10015 date=1140837519]
Only do it if you have 2 dedicated servers and you want to test them. If you have a site on a shared server and run that it will affect all 500 other sites on the server and the hosting company will complain to your ISP or shut your web site down if you're running it from another shared server because port scanning is against the TOS of most hosts (and ISPs)... which won't be fun for you.
[/quote]
Naturally, getting a free security audit from someone else is another option.
http://www.acunetix.com/security%2Daudit/