I dont' know all too much about it, but with the 45nm process you get twice the power in the same space. They are built with differant material giving you better cooling, and more efficient power usage. I have been told by a lot of my friends (who know more than me) to go with the E8400 over the Q6600 for the simple reason it is uses the 45nm technology. Even though you lose the 2 cores, you get all those extra benefits, as for your question whether it's worth $100, you need to ask yourself what your system is going to be used for.
In my opinion you will not regret the $100, I would jump for the better processor. However you won't be disappointed with q6600