In a nutshell, this is what those tuners will do:
They are pre-loaded with either a "canned" tune, which is the manufactures preset tune that basically leans out the fuel curves a little bit, and adds in a certain amount of timing advance. This is really hit or miss - as each car responds different and the parameters may be ok for one car, but not for another. Flash tuners like Diablosport and SCT will let you adjust the generic tunes yourself to a certain degree if you want to tweak the settings.
They can also be flashed with "custom" tunes by a shop that does custom tuning. Often referred to as "mail order tunes", they can actually get pretty accurate because the tuners usually have a lot of experience as to what each car likes to see as far as settings for fuel and spark based upon the mods you have done. Taking it a step further, you can actually datalog the tunes on your car, send them back to a tuner, and have them send you a revised (and even more accurate) tune to flash to your car.
SCT and Diablosport are the two big names in flash tuners. Sniper tuning offers some great tuning options too, but it doesn't seem to have caught on as much (yet).
Speaking personally about the Diablosport tuners, I can adjust these parameters on my car (and more):
WOT timing advance/retard
WOT fuel trim rich/lean
Gear ratio
Fan temp on/off
Shift firmness (auto only)
Rev limiter (drive and neutral)
Speed limiter
MIL indicator on/off
and a few other parameters.
You can't do a full on custom tune yourself with a flash tuner, just adjust a small range of certain parameters. This can help out a lot though, but it's not the ultimate tuning solution.
In addition to being able to tweak settings, you can generally also pull trouble codes (check engine light codes), and datalog a LOT of parameters which can be really helpful.
Hope that helps...
