If you have Cisco hardware you can use NBAR to get the counters. There are some good howto's in the comments section of http://www.ciscoblog.com/archives/2006/05/walking_in_the.html that you'll find useful.
You can also use things such as sflow, netflow, etc to send data to an ntop collector which will graph that sampling. There are also plenty of non free layer 7 graphers out there that like to be put inline. Paul
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