Extreme is the better mobo; even though you lose a SATA port, you have better expansion capabilities. You will also have to weigh out losing 2 USB 2.0 rear ports to get the added eSata and S/PDIF ports as well. Personally, I would take the Extreme and add a USB card or USB drive bay adapter. Given that they're almost the same, the Extreme also has far better reviews.
Ah yea I was wondering about it having less ports and whatnot but it makes since that the might take away a port or 2 for better performance around the same price point. I read somewhere that the Extreme 4 wasn't FX ready and I am going to look into that although I highly doubt it, might need a BIOS update though. I did see alot more and better reviews for the Extreme 3 like you said but I just wanted a second opinion, thanks :-)