I too am curious as to what allegedly makes the later ones more reliable. There are very few actual hardware changes, and it's hard to find any supporting documentation on ones that may (or may not) have been made.
I have heard about the front diff failures. I have read that it was supposedly traced back to a faulty coating on the insides and was phased out by late '05 models (with many of those already replaced by new parts under warranty). I wonder how much of that is true and how much is 'internet true'.
The suspension and roll bar bushings are well known as wear parts to watch - but that effects all years equally.
Other than that, it seems like there was a ton of software updates between the years. Those can be done by the owner with the proper tool.
The '09s look a bit better as they had a new bumper and LR4-ish color coding for some of the LR3s black parts.
IIRC, '05 and '06 lacked lumbar adjustment in the front seats, but was added for '07-'09.
My (bought used) '06 HSE has only needed an alternator and the plastic coolant breather. I've owned it from 63K miles - 94K miles and going.