In my opinion, from what I've read, It's basically:
Q6600 = More Power draw, hotter, older tech
Q8200 = More energy efficient, quieter/cooler, 45 nm
However, This all depends on whether you want to overclock. If it was me, I'd be overclocking, so I'd probably pick the q6600, even if they're not as strong these days (according to above post), the q8200 isn't much for OC'ing. However at stock the difference between the two is negligible, grab the q8200.
As SamSaveMax stated, if you've got the little extra, grab a Q9400. =). Goodluck