For what it's worth, I've been using a combination of things to set my gears.  Time will tell if I've been successful.
Firstly I set FD to as high as it'll go and Top Speed to as low as it'll go.  I then examine each gear and note the min/max.  I have a simple spreadsheet that I use for this.
Column A lists the gears.
Column B lists (what I call) the 'Multiplier'.
Columns C & D show the min and max ratio for each gear.
Column E is derived from B, C & D "=((D-C)/100)*B+C"
I also have three further columns that have formula derived from Scaff's TuningGuidePart2.pdf.  Whilst these three columns are prone to inaccuracy, due to trying to find/guess tyre sizes for any given car, they give you an idea of the speeds you might achieve in any given gear.  Combined with using the results of Column E to make a simple chart, I believe you can make a good stab at setting gears.
Finally, the 'Multiplier' is a simple figure between 1 and 100, a percentage.  I've found that spreading gears exactly evenly can cause problems with the lower gears.  So, for instance, I have an Evo that has the following spread of ratios;
1st	50.0%
2nd	25.0%
3rd	20.0%
4th	20.0%
5th	25.0%
6th	50.0%
This sets my ratios as;
1st	2.989
2nd	2.027
3rd	1.541
4th	1.239
5th	1.047
6th	0.869
With FD set to 4.150, I'm getting the following speeds from each gear (approx);
1st	41.9mph
2nd	61.8mph
3rd	81.3mph
4th	101.2mph
5th	119.7mph
6th	144.3mph
I'm sure there are more scientific ways of doing it, but to be honest, it suits me as I can't afford to get bogged down in the specifics.  I just want to pump some numbers in and then change my Multipliers to get ratios that feel good around a track.  The above Evo ones are for a car that will spend most of its life off road, so I wanted 2nd -> 5th to be quite close with 1st and 6th a bit longer.  Hence my Multipliers.
My Nordschleife LFA has the following spread of ratios;
1st	60.0%
2nd	35.0%
3rd	25.0%
4th	25.0%
5th	35.0%
6th	60.0%
I need more coffee, sorry if the above makes no sense, I hadn't planned on writing it if I'm honest.  Just kinda vomited it out... 
{Cy}