Server :: Sites Being Unaccessible So Many Times In The Day

I have a server with 8GIG of ram and a quad-core q9550 CPU and 500GIG of hard-disk space, and 100Mbps net connection.I have separated it into 3 parts of 2 Gigs of ram each, by virtualization, so there are 3 VPSes. The problem is that the one of the VPSes (created) with centos and WHM/cpanel would go down very often, as many as 60 times per day!I asked one of my friends to have a look at it, and he told me that Tomcat was the reason.Things got a little better (ask me what I changed about Tomcat?!) and after that the server would go down only about 20 to 30 times per day.I asked the friend again, and he told me that the CPanel integrated antivirus would cause the high load periodically.(Ask me again, what did I change?) And after that the server would go down only about 4 to 10 times per day.Now, as far as I can tell, there is nothing more that would/should cause the server to go down.

About 30 minutes ago, before writing this post, the hosted sites were unavailable again, for about 30 seconds.I checked the load through ssh and I saw that the load is 3, so I went to the main server and checked the VPS ram and noticed that only 10% of the cpu is used and only 307Mb of available RAM is used.
Everything shows that the server should be functioning OK, but it still seems to get unavailable far too often.

I used the top command and noticed that there is nothing using the cpu and the ram and all of them are 0.I used the mysqladmin proc command and again nothing noticeably weird seemed obvious at this time. I also checked the other VPSes and they were also in relatively low-resource-consumption states(I don't understand this part):Also sometimes I use the top command when the load goes high I see that all of the users, even the non visitors users site use cpu seems forexample a refreshing things or updating thing updates all of the accounts forexample mysql or so Please help me to figure out what other things might be causing these service/server high loads and unavailability.