Obtain Thinkfan
Download thinkfan from the repositories of your operating system, get it from the upstream website or build your own with the proposed fix for overheating issues.
Before you can use thinkfan, enable fan control of the thinkpad_acpi module.
After installation you'll have to configure it yourself and set your own thresholds and fan levels accordingly.
Danger ahead!
It will not check any settings and you could damage your machine in overheating!
This is what I use on my T61p in the /etc/thinkfan.conf:
sensor /proc/acpi/ibm/thermal (0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
(0, 0, 55)
(4, 48, 60)
(5, 50, 61)
(6, 52, 63)
(7, 59, 76)
(127, 73, 32767)
To enable the daemon, first edit the file /etc/default/thinkfan so that it reads START=yes and start it using
# /etc/init.d/thinkfan start
for Debian, or (Ubuntu)
$ service thinkfan start