Like _YoYo_ said, it all depends on what you want it for.
Personally, I'd lean toward .308 for most applications. There are a lot more semi-auto rifles available at reasonable prices in .308, as well as cheaper milsurp ammo. Being a NATO standard caliber, more ammo is available in more places. At the same time, it's an excellent caliber for long range work in a bolt-action rifle. I'm a big believer in sticking to as few different calibers as possible, so the .308 seems like a great "multi-role" solution.
However, as someone else mentioned, .30-06 has more punch against bigger or harder targets, if that's your deciding factor.
- Dave