I can't be certain on the engines but I think the first may be the older BKD engine which was not without it's faults (although not exactly a dog when you think about how many cars across the VAG range have this engine). They changed to the CR engines around 08 but there was still a 140 and 170 version pre and post 2008 as they are different engines.
I had the BKD 140 unit in my A3, it was faultless and I thought it was very smooth with the DSG box. However, the German specialist indie that I use told me that they get LOADS of them in with turbo failure (fortunately not as costly a repair as with some other cars). Something that the 170 either pre or post CR version doesn't suffer.
I would go for the 170 engine in something the size of the A6. I liked the 140 in my A3 but think it would be a tad weak for an A6. The newer common rail engines are just better and spec wise on the cars it looks like there is nothing in it really apart from Bose which I wouldn't care too much about. If the A3 and A4 are anything to go on then the Bose won't be much better than the standard setup.