Only a minor difference between the two. The 2006 had a little trouble with its rear axle and the 2006-2009 models had possible timing chain issues. If memory also serves, the 2006 auto did NOT have a DPF and the 2007 did.
Timing chains are pretty obvious if they need replacing. They make a huge clattering sound from the front of the motor, it's usually the tensioner that gives out allowing the chain to slap away inside, which can cause the chain to stretch or the chain to start hopping the gears which rips teeth off. It'll cost somewhere around $3K-$5K to replace the chain before it lets go (depending on who does it) and around the $10K mark to fix it if it does let go. They often give warning (but not all the time, had one person report here that theirs let go with no notice at all).
Both models are 126kW 3T towing and no difference really. Real changes came in 2010 with the Thai built ST variant (same engine as the 2006-2009 but missing bits in the loom, indicators in the guard and a couple of vital mm difference in between the chassis rails) and the introduction of the 140kW power plant in the Spanish version, produced by a different head design and an electronically actuated turbocharger control, where the 2006 to early 2010s had vacuum-controlled Garrett GT2056V turbos.
Both cars will need to have a little bit of TLC applied at some point. Vac hoses will be aged and possibly hardened/cracked. Intercoolers will possibly be filled with oil. Fuel hoses may have also begun to perish. Neither will likely be on their original disc rotors because the Nissan ones are made of a special form of Parmesan and generally last just long enough to reach the first major service (40,000km).
It'll also do you good to check and/or replace the brake fluid, diff fluids, check the breather hoses on the diffs, transfer case and gearbox - this applies to either car, they're both around 10 years old.
I'd seriously look at the 2006 model too. My 2009 has just passed 220,000km and is getting a new turbocharger during next week (it should arrive from Forefront Industries on Tuesday). Otherwise it's perfect - and the lower km version should have less wear and tear. It would pay to remove the air hose from the front of your turbocharger, remove the two nuts holding the angled hose retainer and give the impeller a wiggle. It should turn smoothly and not wobble at all. If it does, a new turbo is $800 from Forefront (billet cut impeller, not cast). Reports say better spool times, a couple of people say it boosts harder but Jamie and I had a nice chat and he says it's designed to boost the same as the stock turbo.
That applies to both models, really. As does bearing wear on the front axles - take her for a drive around sweeping left and right corners. As the front end on each side loads up, you'll hear if there's bearing damage, it'll grind a bit.