So, once I have sorted all the little issues out like the emissions light and got the gearbox oil changed  on my '03 3.6, I was wondering what I should do next. I realise that as stock it is a very capable car, and that performance mods are probably not viable engine wise, so what is actually worth doing that makes a difference, but doesn't not mean the other half giving me grief to spending money on my new acquisition?

The simplest thing to increase performance is a remap. The other half won't necessarily tell then ;) 

In my honest opinion I'd keep it stock for the sole reason you a driving a guaranteed future classic! 

Cheers

Steve