Fan-Control-Daemon has been working great for months on my MacBook Pro 8,2 running Ubuntu 13.04 natively but found it getting hotter and hotter all the time. So, I recompiled FCD from source and moved /etc/mbpfan.conf back to default but that really didn’t help. I had to mess with things a little. Of course, you mess with this on your laptop and you could fry it, so good luck to you. I’m not responsible for melted Macbooks.
But, here is my /etc/mbpfan.conf that I am happy with right now. I bumped the max fan speed up from the default of 6200 and messed with the temps a little while changing the check interval to 3 secs.
min_fan_speed = 2000 # default is 2000
max_fan_speed = 8000 # default is 6200
low_temp = 70 # try ranges 55-63, default is 63
high_temp = 85 # try ranges 58-66, default is 66
max_temp = 90 # do not set it > 90, default is 86
polling_interval = 3 # default is 7