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Here are some commonly deleted items and what benefits they bring to the table... also whether or not they actually impact performance:

EGR: EGR reduces the temperature of the combustion chamber (and thus the engine) by routing a small amount of inert gas back into the incoming air flow. This has NO NEGATIVE EFFECT on performance as the valve in this system closes when at high throttle and at idle. It does help the engine cool though before and after hard acceleration. Through clever manipulation of this system many manufacturers (most notably Honda) are able to significantly increase fuel efficiency on engines which still maintain a high peak power output; EGR gases are used to effectively reduce engine displacement when power needs are low and due to the significant reduction in temps they are also able to lean out the fuel mixture to a level which without the EGR would cause severe engine damage.

PCV: This system provides vacuum to the crankcase removing gases which have seeped past the rings as the engine operates. These gases include water (bad for bearings), excess fuel (bad for oil), exhaust gases (caustic: bad for EVERYTHING)... etc. A healthy PCV system actually HELPS rings seal. The ONLY downside to this system is that over a couple dozen thousand miles some oil may accumulate in the intake and you'll want to clean it out. If it's accumulating more quickly then consider it a free diagnosis of your rings' health... but the problem is not with the PCV system and is readily solved by installing a catch can.

Charcoal EVAP Canister: A simple canister which collects gasoline which would otherwise just evaporate out of your gas tank and actually saves them until they can be slowly trickled back into the engine. You can lose well over a gallon of fuel in a week otherwise... again... NO NEGATIVE EFFECT. Back when gas was under a buck per gallon the whole "but it ain't purdy" argument sounded a lot less stupid, but today.... sorry... they might as well write dumbass across their forehead

Intake Helmholtz Resonator: A VERY simple air reservoir (on 7M-GE and other Toyota engines not on the 7M-GTE though) which serves to reduce turbulence in the intake charge... It does also quiet down the intake sounds but that's only half the reason for it's inclusion; It's been proven that a true Helmholtz resonator can actually restore a significant amount of power that would otherwise be lost due to turbulence in the airway. Helmholtz resonators are not restrictive at all.

Exhaust Helmholtz Resonator (not to be compared or confused with the garbage, baffle based, mini mufflers that are only used for noise reduction purposes): Like their counterpart in a tuned intake these devices quiet an exhaust (and make it sound less farty like a Honduh or 7M-GE with a turbo exhaust) by removing significant amounts of turbulence. This promotes stronger scavenging of cylinders reducing the need for the engine to expend power to push these gases out. Depending on the cam profile this can also be used to create a stronger initial vacuum to help pull in the following intake charge (this continues into the benefits of a properly sized exhaust system and how bigger is NOT better). Again: NO NEGATIVE EFFECT