I am looking for a utility (Windows/Linux/Mac) that will allow me to run some test packets across a customer's network (between their client & my server) to identify a list of (or at least a guess of) all protocols and significant network settings that could adversely effect my systems performance in their eyes...

Description of the Scenario -
Problem: A client machine gets poor performance when accessing data from a server.
Response: Must be something wrong with the server.
Actual Cause: Network overhead because of the core router imposing some rule to my traffic that I was unprepared for.
Fix: Check for all imposed rules between end nodes & compare to list of known trouble-causers, alerting customer of incompatibility

Any ideas?

Search the internet for iperf - it's a TCP profiler, very useful tool.