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This is a brief overall synopsis of what can be 'tuned' or altered and what tuning is (taken from HP Tuners website):
Here is just a basic summary of some of the things you can edit with our package. A complete list would be quite lengthy.
The exact parameter set for your particular application may be different. Due to the number of applicaitons we support, we cannot list all of the supported parameters on a per application basis.
Engine
EGR, Air Pump, COT Enable/Disable and controls
Rev Limiters, Idle Speed and characteristics
Throttle Follower and Cracker
MAF Tables, Main VE and Cranking VE
Power Enrich fuel controls
Closed Loop/Open Loop characteristics
Injectors
Spark Advance and Retard