A lot of site and places I go to that programs PCM give you the options to also have certain features programmed as well such as


Torque Management Delete
Disable EGR
Disable AIR
Disable VATS
Disable EVAP
Disable Rear O2 sensors
Disable CAGS (skip shift)
And
High octane power programming (91+ octane)

 

Torque Management Delete - Torque management pulls timing during the shift to protect the transmission. When you have this disabled it doesn't. Generally when people put in a shift kit and servos they will have TM taken out.

Disable EGR - Allows you to remove your EGR system without throwing codes.

Disable AIR - Allows you to remove your AIR system without throwing codes.

Disable VATS - Not really sure why you would do this one unless it's causing you problems

Disable EVAP - I guess this allows you to remove your EVAP solenoid and just run a breather off the evap line.

Disable Rear O2 sensors - Allows you to remove cats without throwing codes

Disable CAGS (skip shift) - Disables annoying skip shift
And
High octane power programming (91+ octane) - More power available when running high octane gas (I think they just add more timing on a 91 tune)

 

Torque Management Delete-better shifts and no timing pulle don shifts or abuse mode

Disable EGR-get rid of it on 98-00 cars , no code when its removed

Disable AIR-same as egr but 98-02

Disable VATS-so you dont need a chip key to start the car, mainly conversions into olde rcars

Disable EVAP-just get rid of codes for equipment that isnt there anymore in some cas

Disable Rear O2 sensors-needed to be done after the cats have been eliminated

Disable CAGS (skip shift)6speed cars are forced to shift 1st to 4th under light throttle unless this is bypassed/shutoff

And
High octane power programming (91+ octane)-this is the fuel and timing maps tadjustments that get you more power