Thanks for your replies. I'm still deciding. I think:
Intel: great control with supplied software. CPU fan must be PWM (my fans are Nexus three pins).
Gigabyte: Three pin control on CPU fan and sys1 fan. Sys 2 & 3 PWM only.
Looks like people have had some trouble setting up the Gigabyte boards with speedfan, but this thread shows it can be done: http://hardforum.com/showthread.php?t=1742628
If I can afford it I'm leaning towards the Intel board, mainly because the SPCR review says speed fan works and if it doesn't the supplied software is good (although I want to find out if the minimum fan setting includes zero!).