As soon as I read your question, I instinctively have to ask what kind of gear you are using.
Switches? Hubs? And what types/brands? (the branding question is important because there are "pseudo crapo switches*" like the stuff you buy at BestBuy or Staples and then there exists real switches, like Cisco for example).
*Note: The switches you buy at Best Buy are great for home use, I bought my wireless router there actually. But for commercial grade networking you need the more feature rich and proven realiability of a higher end switch than what those stores offer, that is what I was saying.
Routers?Gateways?
I'd look at your hardware first is what I'm saying, then if you have good (healthy) gear that is configured properly, look at your cabling. If the cabling is in good shape and tests fine, then look into software issues.