Network Diagnostic Assistance

There are so many monitoring tools you can use to identify.

You can use Wireshark to monitor network traffic.If you have a managed switch that supports port mirror then you can use Wireshark:
http://www.wireshark.org/download.html

The following link will give you idea how to do it:
http://www.immonitor.com/netgear-port-mirroring.htm

Alternatively, you can also can use Ethreal.

Or, if you use Cisco then you can use Netflow Analyzer to analyze Network traffic.You also  can use Cacti or MRTG to check your switchport usage if your switch supports SNMP.
http://www.cacti.net

And for Microsoft server you can use Netmon which is a protocol analyzer by Microsoft:
http://www.microsoft.com/download/en/details.aspx?displaylang=en&id=4865

There are other popular tools: PRTG(Free up to 10 sensors), Whatsup Gold, Solarwinds etc.But these are commercial software.

Doing a packet capture and analyzing it with WireShark is a good thing. Also Cacti http://cacti.net/ is a brilliant software to narrow down the problem,
I would  monitor and troubleshoot Performance Issues of the network devices (cisco):
show cpu
show traffic
show perfmon
show blocks
show memory
show xlate
show conn count
show interface
show processes