Thanks to the below link, I was able to turn down the annoying fans on my old Sony PCV-RX650 while running Ubuntu:
http://ubuntuforums.org/showthread.php?s=f65942f674eb3572c64c294ca6810608&t=238566&page=2
This problem has been bugging me and preventing me from running Linux on this system. I’m glad I was able to resolve this problem without having to upgrade the BIOS (~ $30) to have the latest ACPI 2.0 feature (currently it has APM).
I first found out that I need to activate the root password on Ubuntu by running “sudo password root”, this allows me to act like root.
I then followed the instructions of getting and installing  the lm_sensors package first by running “sudo apt-get install lm-sensors”
run: sensors-detect (answered “yes” to all of their questions)
This basically add the following lines to /etc/modules:
#====================================
# Generated by sensors-detect on Thu Aug 23 23:44:40 2007
# I2C adapter drivers
i2c-i801
# Chip drivers
eeprom
w83627hf
#====================================
reboot to have the modules loaded
run: pwmconfig
to set the preferences
you can try to run fancontrol at this point as root to see if it is working.
Finally add a line below to to /etc/rc.local (to allow for auto execution upon power up)
/usr/sbin/fancontrol &
Below is the transcript of what I did:
======================================================
dtsai@ubuntu:~$ sensors
w83637hf-isa-0290
Adapter: ISA adapter
VCore:     +1.74 V  (min =  +0.71 V, max =  +0.70 V)       ALARM
+12V:     +11.92 V  (min =  +0.00 V, max =  +3.89 V)       ALARM
+3.3V:     +3.36 V  (min =  +2.24 V, max =  +0.51 V)       ALARM
+5V:       +5.15 V  (min =  +0.00 V, max =  +0.21 V)       ALARM
-12V:      +6.06 V  (min = -14.91 V, max =  -4.14 V)       ALARM
V5SB:      +5.08 V  (min =  +0.00 V, max =  +3.44 V)       ALARM
VBat:      +0.00 V  (min =  +0.00 V, max =  +2.06 V)
fan1:     4530 RPM  (min = 16071 RPM, div = 2)              ALARM
CPU Fan:  2265 RPM  (min = 168750 RPM, div = 4)              ALARM
fan3:        0 RPM  (min =   -1 RPM, div = 2)              ALARM
M/B Temp:    -48°C  (high =   +33°C, hyst =  -127°C)   sensor = thermistor
CPU Temp:  +38.5°C  (high =   +80°C, hyst =   +75°C)   sensor = diode
temp3:     +34.0°C  (high =   +80°C, hyst =   +75°C)   sensor = thermistor
vid:      +1.550 V  (VRM Version 9.0)
alarms:
beep_enable:
          Sound alarm enabled
dtsai@ubuntu:~$ pwmconfig
This program will search your sensors for pulse width modulation (pwm)
controls, and test each one to see if it controls a fan on
your motherboard. Note that many motherboards do not have pwm
circuitry installed, even if your sensor chip supports pwm.
We will attempt to briefly stop each fan using the pwm controls.
The program will attempt to restore each fan to full speed
after testing. However, it is ** very important ** that you
physically verify that the fans have been to full speed
after the program has completed.
Found the following PWM controls:
   9191-0290/pwm1
   9191-0290/pwm2
   9191-0290/pwm3
Found the following fan sensors:
   9191-0290/fan1_input     current speed: 4530 RPM
   9191-0290/fan2_input     current speed: 2280 RPM
   9191-0290/fan3_input     current speed: 0 … skipping!
As you are not root, we cannot write the PWM settings.
Please run as root to continue.
dtsai@ubuntu:~$ su root
Password:
root@ubuntu:/home/dtsai# pwmconfig
This program will search your sensors for pulse width modulation (pwm)
controls, and test each one to see if it controls a fan on
your motherboard. Note that many motherboards do not have pwm
circuitry installed, even if your sensor chip supports pwm.
We will attempt to briefly stop each fan using the pwm controls.
The program will attempt to restore each fan to full speed
after testing. However, it is ** very important ** that you
physically verify that the fans have been to full speed
after the program has completed.
Found the following PWM controls:
   9191-0290/pwm1
   9191-0290/pwm2
   9191-0290/pwm3
Found the following fan sensors:
   9191-0290/fan1_input     current speed: 4470 RPM
   9191-0290/fan2_input     current speed: 2265 RPM
   9191-0290/fan3_input     current speed: 0 … skipping!
Warning!!! This program will stop your fans, one at a time,
for approximately 5 seconds each!!!
This may cause your processor temperature to rise!!!
If you do not want to do this hit control-C now!!!
Hit return to continue: 
Testing pwm control 9191-0290/pwm1 …
  9191-0290/fan1_input … speed was 4470 now 0
    It appears that fan 9191-0290/fan1_input
    is controlled by pwm 9191-0290/pwm1
Would you like to generate a detailed correlation (y)? y
    PWM 255 FAN 4530
    PWM 240 FAN 4500
    PWM 225 FAN 4272
    PWM 210 FAN 4115
    PWM 195 FAN 3857
    PWM 180 FAN 3688
    PWM 165 FAN 3426
    PWM 150 FAN 3199
    PWM 135 FAN 2973
    PWM 120 FAN 2710
    PWM 105 FAN 0
    Fan Stopped at PWM = 105
  9191-0290/fan2_input … speed was 2265 now 2265
    no correlation
Testing pwm control 9191-0290/pwm2 …
  9191-0290/fan1_input … speed was 4470 now 4383
    no correlation
  9191-0290/fan2_input … speed was 2265 now 0
    It appears that fan 9191-0290/fan2_input
    is controlled by pwm 9191-0290/pwm2
Would you like to generate a detailed correlation (y)?
    PWM 255 FAN 2280
    PWM 240 FAN 2280
    PWM 225 FAN 2265
    PWM 210 FAN 2265
    PWM 195 FAN 2205
    PWM 180 FAN 2149
    PWM 165 FAN 2070
    PWM 150 FAN 1985
    PWM 135 FAN 1896
    PWM 120 FAN 1814
    PWM 105 FAN 1704
    PWM 90 FAN 1607
    PWM 75 FAN 1500
    PWM 60 FAN 1383
    PWM 45 FAN 0
    Fan Stopped at PWM = 45
Testing pwm control 9191-0290/pwm3 …
  9191-0290/fan1_input … speed was 4470 now 4500
    no correlation
  9191-0290/fan2_input … speed was 2265 now 2280
    no correlation
No correlations were detected.
There is either no fan connected to the output of 9191-0290/pwm3,
or the connected fan has no rpm-signal connected to one of
the tested fan sensors. (Note: not all motherboards have
the pwm outputs connected to the fan connectors,
check out the hardware database on http://www.almico.com/forumindex.php)
Did you see/hear a fan stopping during the above test (n)? 
Testing is complete.
Please verify that all fans have returned to their normal speed.
The fancontrol script can automatically respond to temperature changes
of your system by changing fanspeeds.
Do you want to set up its configuration file now (y)?
What should be the path to your fancontrol config file (/etc/fancontrol)?
/etc/fancontrol does not exist, shall I create it now (y)?
Loading configuration from /etc/fancontrol …
Select fan output to configure, or other action:
1) 9191-0290/pwm2      3) Change INTERVAL     5) Save and quit
2) 9191-0290/pwm1      4) Just quit           6) Show configuration
select (1-n): 6
Common Settings:
INTERVAL=10
Settings of 9191-0290/pwm2:
  Depends on
  Controls
  MINTEMP=
  MAXTEMP=
  MINSTART=
  MINSTOP=
Settings of 9191-0290/pwm1:
  Depends on
  Controls
  MINTEMP=
  MAXTEMP=
  MINSTART=
  MINSTOP=
select (1-n): 1
Current temperature readings are as follows:
9191-0290/temp1_input   -48
9191-0290/temp2_input   36
9191-0290/temp3_input   34
Select a temperature sensor as source for 9191-0290/pwm2:
1) 9191-0290/temp1_input
2) 9191-0290/temp2_input
3) 9191-0290/temp3_input
4) None (Do not affect this PWM output)
select (1-n): 3
Enter the low temperature (C)
at which the fan should be switched off (0): 32
Enter the high temperature (C)
at which the fan should be switched to full speed (60): 
Enter the minimum PWM value (0-255)
at which the fan STARTS spinning (press t to test) (150): 
Enter the minimum PWM value (0-255)
at which the fan STOPS spinning (press t to test) (100): 
select (1-n): 2
Current temperature readings are as follows:
9191-0290/temp1_input   -48
9191-0290/temp2_input   35
9191-0290/temp3_input   34
Select a temperature sensor as source for 9191-0290/pwm1:
1) 9191-0290/temp1_input
2) 9191-0290/temp2_input
3) 9191-0290/temp3_input
4) None (Do not affect this PWM output)
select (1-n): 3
Enter the low temperature (C)
at which the fan should be switched off (0): 32
Enter the high temperature (C)
at which the fan should be switched to full speed (60): 
Enter the minimum PWM value (0-255)
at which the fan STARTS spinning (press t to test) (150): 
Enter the minimum PWM value (0-255)
at which the fan STOPS spinning (press t to test) (100): 
select (1-n):
1) 9191-0290/pwm2      3) Change INTERVAL     5) Save and quit
2) 9191-0290/pwm1      4) Just quit           6) Show configuration
select (1-n): 6
Common Settings:
INTERVAL=10
Settings of 9191-0290/pwm2:
  Depends on 9191-0290/temp3_input
  Controls 9191-0290/fan2_input
  MINTEMP=32
  MAXTEMP=60
  MINSTART=150
  MINSTOP=100
Settings of 9191-0290/pwm1:
  Depends on 9191-0290/temp3_input
  Controls 9191-0290/fan1_input
  MINTEMP=32
  MAXTEMP=60
  MINSTART=150
  MINSTOP=100
select (1-n): 5
Saving configuration to /etc/fancontrol…
Configuration saved