I've read all the stuff listed above. That's the beginning of how to tune and it's all very useful information compiled by guys who have nothing to gain but the satisfaction of sharing their accumulated knowledge about the game. Without them, and without the recurring arguments and discussions about tuning that pop up frequently, most of us would be in a tuning fog, me included. Settle in for lots of reading, take some notes or print some of it off. You have to then take that information, take a car to the track, and spend time making adjustments and see what happens.
I would suggest three ways to do this. Take a car you like that's already a good handling car and not too overpowered so you aren't worried about constantly maintaining control. I'd suggest 450-500pp on sports tires to begin with. The RX-8 Type S 07' is a good car for this and in fact, I'd start with one that is already well tuned so you can get an idea of the range of settings on a car that makes it work well. I believe it's easier to start with something good and then move away from it in one direction or another, rather than starting from scratch and trying to make something work. Remember, at this point you're simply trying to figure out what every setting does, not trying to tune a whole car.
Make one adjustment at a time to it and take it out on the track. Write down what effect it seems to have. Back to the pits, readjust the same setting or reset that adjustment and move on to something else, and make another adjustment. Don't be afraid to make some leaps here. You don't have to take the suspension stiffness from 9.8 to 9.7 to 9.6. It's ok to go from 9to 8 to 7.
If you really want to learn about tuning, it takes time, a lot of time. Not trying to scare you but we're talking hundreds and hundreds of laps of testing before you really begin to get a feel for it. Then when you think you've got a feel and you're all cool, you'll find someone else's tune for a car, drive it, figure out yours is crap and realize you've just scratched the surface and aren't as good as you think you are.
Second thing to do is to begin tuning cars. Once you get a feel for how the adjustments work, take some cars that you like to drive and begin tuning. I suggest a couple of different tracks, one relatively flat like Monza or Road Course Indy or Tsukuba and one hilly with varied camber like Deep Forest or Trial Mountain. Tune for the flat courses first as it's easier, then come to the bumpy/hilly course and make adjustments if necessary. Finding something that is good on both is tricky and often serious racers/tuners will have different tunes for each kind of track.
Third thing I'd do is enter a tuning competition. There is always at least one F.I.T.T. contest going on at some point and others appear to be popping up here and there. It will cause you to intensely focus on one car/track/tire combination, and testing various cars to see which one you like. Then it's trial by fire, meaning, can anyone else drive your tunes, or are they suited to your driving style. Their feedback is one of your best tools. 10-15 people or more will scrutinize your tune and some may love it and some may hate it, but you will learn something no matter what the outcome.
Also, Scaff has a guide linked up there in the stickies somewhere that goes pretty in depth about what is doing what. It was written for GT4 for the general knowledge still applies since physics doesn't change out in the real world. 
