The single biggest change is that the '06 GTs have the powered brakes, while the later years don't.
The '07 and newer bikes had additional options, such as ASC, TPM, HID, etc.
There were also a number of small changes made over '06, '07, and '08 to enhance reliability and comfort. Things like a different seat, cam chain tensioner, clutch bits, oil tank cap, air box, and of course, various software upgrades.
And of course, some color changes over the years, most notably that Crystal Grey Metallic ('06-'07) was changed to Aventurine Silver ('08).
None of these by itself is a deal-breaker (except maybe the air box), but there are still some advantages to getting as new a bike as you can afford. Plus having a good dealer to take care of those thing particular to your bike is invaluable.
'13 Dark Graphite Metallic K16GTLD, 24K miles and counting...
'09 Magnesium Beige Metallic K13GT, 60K miles miles and counting...
'02 Mauve Metallic K12LTC, 106K miles and sold
BMWLT#145, IBA# 366, MOA# 111996, SCMA# 24032
All lower 48 states plus Alaska on the K13GT in two weeks . . .
Some people see the gas tank as half empty. Some see it as half full. All I care is that I know where the next tankful is coming from...