In what may be a surprise, the Pac-10 has the highest average ahead of the SEC. The Big-12, Big-Televen, and ACC fall in behind and what isn't a surprise is that the Big-East trails all other BCS conferences.
Why is the Pac-10 ahead of the SEC right now? Simply put, it comes down to schedule strength to this point. The average schedule strength for Pac-10 teams is 69.014 right now compared to 66.950 for the SEC. That over 2 point gap is actually slightly greater than the gap between average team ratings so if the SEC had played a similar schedule to this point they'd likely be #1. Also, the one direct connection between the conferences had Oregon thumping Tennessee.
Why is the schedule strength that much lower? It is primarily because the Pac-10 has played against teams like Nevada (#4), TCU (#6), Iowa (#10), Boise St (#12), Nebraska (#15), Oklahoma St (#26), and Texas (#30) while the SEC has only played Oregon (#5), Clemson (#21), Penn St (#24), and Northwestern (#29).
The Pac-10 certainly has highs and lows in their ratings though with WSU being the worst at #103 while the SEC worst is only #79 Tennessee.