If your version of IOS supports it, take a look at the ip sla feature on cisco routers. It will provide the most accurate packet loss, latency and jitter results.
Here is an introductory page.
http://www.cisco.com/en/US/tech/tk920/tsd_technology_support_sub-protocol_home.html
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Here's another similar <a href="http://itknowledgeexchange.techtarget.com/itanswers/ip-sla/">question/answer</a> with more details.
Last Wiki Answer Submitted: October 23, 2008 7:16 pm by Peterp270 pts.
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This is a good tutorial to get you started with what you are trying to accomplish:
http://www.networkworld.com/community/node/30924