First off, this isn't the import world so there is no stage 1, 2, 3, etc...
As others have said, there are:
1. "Canned" tunes, referring to an 'as is' tune that comes on a programmer. These are meant to cover a broad range of customers and generic modifications. They are not completely optimized but often make more power than stock and improve driveability. They will require a minimum octane of fuel for the tune and are identified in the nomenclature. These tunes work for all calibration strategies for that make or model and can be used right out of the box.
2. Email tunes:. The basic version usually does not require data logging and is a tune that has been developed by a custom tuner for a given set of modifications such as a specific brand of supercharger, injectors, MAF, etc...
3. The next level is email tuning with datalogging. This allows tuners to optimize timing and fueling for the specific fuel you are using, your injectors, MAF, etc... You will often be able to change things like throttle response, cold start behaviour, and correct small driveability issues.
4. Dyno operator tune: This is with the vehicle on the dyno and mostly focuses on WOT tuning. This will often give good power numbers but gets very expensive for tuning driveability as you are often paying for the dyno time as well. Advantage is that you will often work with the tuner in person but you have to live somewhere that is close to someone that you trust tuning your vehicle.