Transmission tuning is of the most subjective parts, second only to the LSD. Driving style dictate your ideal setup as much as the track/car you're driving. Playing around with outrageous gear setups will hastily teach you what is wrong/right for the middle gears, like 2nd, 3rd and 4th. Which you'll spend most of your time in anyways.
For Example, In a 350hp car on Sports Hard tires:
If a mid-speed section of the with a lot of turns you would generally want a wider gear setup for that part of the cars speed range. Such as a wide 3rd gear will range from 60mph-90mph in most 6-speed trannies or 65mph-100mph on 5-speeds. That wat you would go through that mid-speed section without losing time from shifting up to 4th gear in that section. You would generally want a narrower 4th gear since high speed sections in most tracks won't have you going past 120mph for more than 2 seconds before having to slow down for a low/mid speed corner. That narrow gear you be close and accelerate to redline rather fast and using the top end of the car's powerband.
Take this example and adjust it for the car you have in mind. Take into account horsepower, torque and the powerband.. That graph on the tuning setup page that shows you what RPM range the vehicle makes torque and horsepower. Lowest gears you would generally want wide for acceleration and to avoid major wheelspin. It's all up to you! Gran Turismo lets you tune till your heart's content.
Now... with LSD. It is the most subjective of tuning parts because it depends on your style more so than the other parts. Suspensions can be adjusted for personal style but there is generally a few rules that apply to suspension tuning for different events. Rally, Drift, Touge, Track/Circuit, etc. That.. and LSD tuning philosophies don't apply the same to most cars. Not every MR will react the same with similar setups. Most 4WD act alike with a few exceptions. FF are my weakest point at the moment. FR are the most predictable of the lot.
Again the power band comes into play. Ask yourself these questions as you tune your car's LSD
how much power and torque my car makes?
when does my car make this power (as in during which PRMs)?
is there a dip in the torque band? a hill? a plateau? or a peak.
how drastic is the torque band's elevation/drop?
When does my car make horsepower? as well as the other questions pertaining to torque ^^
Now, the question that makes or breaks your setup is...
During which RPMs am I going to be driving the car the most in this track/type of track??
While 'trying out your own numbers notice if the car is under/over steering and adjust accordingly.
GT5 makes available the parts/tuning manual in online mode now. Meaning when you're tuning your car, click the yellow question mark (?) above the settings of each part for a brief yet detailed explanation of what each change each adjustment would make.
Above All, Practice.
If you would take the time, feel free to send me a friend request. I usually host private lobbies with friends and drive and tune together and show off our cars. You could learn a thing or two hanging around. Also, my tuning thread is a side-project of mine I update on my free time to share my setups and style.
I've got another one fresh from the UCD for you to keep, so can I has my Yellow Spoon back now? I'll give you a sliver spoon in return. 
