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To answer your question directly, the BEST equipment to tune your car is whatever piggyback or standalone you can have tuned confidently by someone local to you. No sense buying a MoTeC M800 (for example) if nobody within a 10 hour radius can tune it properly for you. Also, there's no point having way more ECU than you need (why buy MoTeC when Megasquirt works just fine for what you need to do).
As for software, it all depends on the ECU in the car.
An AEM will use AEM's software.
A MoTeC will use MoTeC software.
Etc, etc, etc
Not sure if piggy-back units like the Apexi Power FC use external software or not.... I recall "Power Excel" being tossed around, but I believe that's only available to licensed/trained Apexi dealers.
So basically, with a skyline, you have a metric-sh*t ton of options for tuning.
As for tuning other applications (I'm assuming you mean other vehicles), it's not like OBD-2 Diesels where you can run your Edge tuner and get an extra 200HP out of your vehicle... whatever HARDWARE you buy to tune a Skyline, you're pretty much stuck using it on a Skyline (maybe other Nissans if it's a piggy-back). Software can be used to tune any car with an ECU that uses the same software.
You can buy Nistune, Nistune tuning software (has Consult, Consult gauges, etc built into tuning software), cheap netbook (with solid state hard drive, as it does get knocked around when tuning and make sure it has 2x USB ports for USB Consult cable, USB wideband), USB Consult tuning cable (from Nistune which stops connection from dropping out when tuning and has connection, transfer light's on it).
Netbook can be used with their tuning software (Link, Motec, etc). But if can find one, tablet PC would be easier and can mount in car as a MFD (Multi Function Display), like found on R34GTR. But can change tune, etc with Nistune tuning software, which can't be done with R34 MFD.
ECU is chosen based on what you are doing with car (street, racetrack, drag, etc) and budget. For street, occasional trackdays, low budget, stock ECU with Nistune works (also don't need to tune straight away if have say intake, exhaust mods), but need to buy boost controller, etc. If want better drivability, want to datalog shock damping, rebound, rpm, speed, etc, for race use, then Motec is used (usually on racecars, drag cars, but sometimes on street cars with Targa rally, etc).
Link G4 ECU, ViPEC ECU are good low budget topend ECU options and don't require a boost controller (onboard boost control). Both work with Skylines. Not as good as Motec in terms of how many adjustment rows with rpm (dragcar engines), running aftermarket ignition module, running fly by wire TPS setup, datalogging shock rebound, damping, traction control, etc, but do a good job.
If you use a powerFC you can get the FCdatalogit module which comes with tuning software , you can also replace that software with co=-pilot available free on the net that can autotune your fuel maps and also ignition map.
Vipec comes with software that can selftune fuel if you have a wideband hooked up , can also autotune timing if you have a digital knock amp setup .
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