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1. Group them in one VLAN as possible
Identify which computers that most of the time access particular servers. Then group all of those computers and the associated servers in one VLAN as possible.
2. Setup dedicated VLAN for servers only when necessary
When you have users from multiple departments accessing one specific server, then put this particular server in dedicated VLAN. Do not put regular non-server computer into this VLAN due to security vulnerability.
3. "Minimize Distance" between computers
Whenever possible; put all hosts (computers, servers, printers, etc.) in one single switch. When all of the hosts are spread into multiple switches, shorten the distance between switches. Especially for high traffic or critical application, use the largest bandwidth possible to "minimize distance" between hosts.
We use a switch with 24 ports of 10/100 Mbps speed and 2 ports of 10/100/1000 Mbps speed. Should we use the Gigabit port to connect to servers and use Fast Ethernet ports as trunk?
When you have hosts spread into multiple switches, then you should use the Gigabit-capable port to connect to servers and 10 Gigabit-capable port as trunk (of course whenever possible).
Keep in mind that as general idea, should always use the fastest port available as trunk when there are hosts spread into multiple switches. Do not, as example, use Gigabit port for server connections and Fast Ethernet port as trunk in this multiple switches situation since the traffic across switches are bogged down at the trunk (the trunk causes "bottleneck"). It is then better to use the Fast Ethernet port for server and the Gigabit port for trunk.