I've been offered a lovely 2.0 TDI, 2008 B7 S-line avant with a blown engine. The engine code is BRE and the gearbox is JEM. What do you think, would it be more trouble than it's worth, is the BRE engine just rubbish and is there a reasonable alternative?

Speaking as someone with a wrecked engine on a a6 c5, unless you get an engine with an identical engine code you'll have to code any different engine to the ECU, injection pump and instrument cluster. At least that's the case with my A6. My A6 has a one year only version of the 2.5 and finding another has been a nightmare.