Slow Throughput Through Network

What kind of switches? Could be a duplex mismatch between the switch port and the server NIC...

>The network cards are configured at their top speed (either 1GB or 100MB) and Full Duplex.
That could be a problem. If the switches are unmanaged, meaning you can't go in and set the switchport to match, then you have a duplexing issue by nature of how the negotiation works.
With unmanaged switches, you must set NIC to auto both speed and duplex.
Here's what happens otherwise.
Switchport set to auto (only setting on non-managed switch)
Switchport expects duplex negotiation packet
NIC set to 100/full-duplex
NIC does not send negotiation packet, negotiation has been disabled
Switchport does not get a negotiation packet, but knows something has been plugged in
Default switch behavior says that if you get a link and no negotiation packet, then it must be a hub and all hubs are half-duplex, therefore set interface to half-duplex.
Now the switch port is at half-duplex and the NIC is at full duplex and the end result is that you get horrible performance.

her's a couple other things I've run across over the years

Speed up your browsing of Windows 2000 & XP machines AND Speed up viewing shared files across a network

Here's a great tip to speed up your browsing of Windows 2000 & XP machines.
Its actually a fix to a bug installed as default in Windows 2000 that scans shared files for Scheduled Tasks.
And it turns out that you can experience a delay as long as 30 seconds when you try to view shared files across a network because
Windows 2000 is using the extra time to search the remote computer for any Scheduled Tasks.
Note that though the fix is originally intended for only those affected, Windows 2000 users will experience
that the actual browsing speed of both the Internet & Windows Explorers improve significantly after applying it
since it doesn't search for Scheduled Tasks anymore.
Here's how :

Open up the Registry and go to :

HKEY_LOCAL_MACHINE/Software/Microsoft/Windows/CurrentVersion/Explorer/RemoteComputer/NameSpace

Under that branch, select the key :{D6277990-4C6A-11CF-8D87-00AA0060F5BF} and delete it.

This is key that instructs Windows to search for Scheduled Tasks.
If you like you may want to export the exact branch so that you can restore the key if necessary.

This fix is so effective that it doesn't require a reboot and you can almost immediately determine yourself how much it speeds up your browsing processes.

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BONUS TIP#2

Windows XP automatically searches the network for shares and printers upon connecting to the network. This is probably useful in a SOHO or home network but not the enterprise. To disable XP automatic discovery:
In Explorer, click Tools
Click Folder Options
Click the View tab,
Uncheck Automatically Search for Network Folders and Printers in Advanced settings list.
 
It is important to disable this setting in Windows XP because it is the basis of a seriouse security flaw in XP. When you click My Network Places, your logon password may be transmitted automatically to numerous unspecified computers on the LAN. Windows XP tries to acquire the shared resources list of all computers on the LAN. At that time, the users local logon password is used when the password for the shared resource is not known. Your PC transmits the LMhash version of you password.

If there are NT4.0 or any other pre-Windows 2000 PCs on the LAN, XP will transmit your password to the pre-Windows 2000 PCs during its share and print search. It transmits the LM hash which is significantly weaker than XP or Windows 2000 hashes. In order to protect the LM hash, XP has a registry value HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Lsa\NoLMHash which if set to 1 will prevent XP or Windows 2000 from generating the LM hash. pwdump will not be able to acquire the LM hash, which is a good thing.

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Network troubleshooting

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Hidden in Windows XP's System Information utility is a very good tool for getting a lot more information about what's going on. Go to Start | All Programs | Accessories | System Tools | System Information. Then choose Net Diagnostics from the Tools menu. The program will ping your DNS servers, gateways, SMTP and POP3 mail servers, and proxies; test your modem and network adapters; and supply very detailed reports about your settings, as well as which tests passed and which failed.