Here you can find a listing of motherboards that users like you reported as being able to change fan speeds. This is a subset of the hardware that SpeedFan can properly work with. Please note that this is not the listing of the motherboards where SpeedFan is able to access readings from temperature sensors and S.M.A.R.T. hard disks. As an hardware monitoring tool, SpeedFan can work almost on every hardware. I do add new references here based on several reports from end users. If you are going to report a new motherboard, please tell me (at changes [at] almico.com) about how smooth the control is. If the control looks like an ON/OFF one, please, have a look at the "What is PWM and how is it used to control fan speeds?" article and check the PWMOUT option (if any) in CONFIG / ADVANCED.
Disclaimer: I'm doing my best to keep this list up to date and as reliable as possible. Don't blame me if the revision of the motherboard you've purchased can't change fan speeds the way you hoped :-)

Manufacturers ABIT 101 ACER 2 ACORP 68 ALBATRON 146 AOPEN 43 ASROCK 57 ASUS 204 BIOSTAR 78 CHAINTECH 6 COMPAQ 3 DELL 8 DELTA 1 DFI 17 ECS 21 EPOX 10 EVGA 2 FIC 5 FOXCONN 4 FUJITSU/SIEMENS 3 GIGABYTE 48 HP Compaq 3 IBASE 1 IBM 4 INTEL 17 IWILL 5 JETWAY 1 KOBIAN 2 MATSONIC 1 MERCURY 1 MSI 62 PROCOMP 1 QDI 6 QUANTA 1 SAPPHIRE 1 SHUTTLE 26 SOLTEK 5 SONY 9 SOYO 8 SUPERMICRO 2 TOSHIBA 1 TRANSCEND 1 TRIGEM 2 TYAN 8 XFX 1

Motherboards from GIGABYTE that can change fan speeds Manufacturer Model Chipset CPU Notes GIGABYTE GA-6OMM7 Intel 815 FC-PGA GIGABYTE GA-6OXC Intel 815EP FC-PGA GIGABYTE GA-6OXE Intel 815EP FC-PGA GIGABYTE GA-6OXM7E Intel 815E FC-PGA GIGABYTE GA-6WMMC7C Intel 810 FC-PGA GIGABYTE GA-7N400 Pro nForce 2 Ultra Socket A GIGABYTE GA-7N400 Pro2 nForce 2 Ultra Socket A GIGABYTE GA-7N400-L nForce 2 Ultra Socket A GIGABYTE GA-890FXA-UD5 (rev. 2.1) AMD-890FX AM3 GIGABYTE GA-8I875 Intel 875P Socket 478 GIGABYTE GA-8I915G-MF Intel 915G LGA775 GIGABYTE GA-8I915P Duo Pro Intel 915P LGA775 GIGABYTE GA-8I945GMMFY-RH Intel 945GM Express Socket 479 GIGABYTE GA-8I955X Royal Intel 955X LGA775 GIGABYTE GA-8IDX Intel 845 Socket 478 GIGABYTE GA-8IK1100 Intel 875P Socket 478 GIGABYTE GA-8IPE775 Pro Intel 865PE LGA775 GIGABYTE GA-8KNXP Intel 875P Socket 478 more... GIGABYTE GA-8TX Intel 850 Socket 478 GIGABYTE GA-965P-S3 (rev. 3.3) Intel P965 Express LGA775 GIGABYTE GA-EG45M-UD2H (rev. 1.0) Intel G45 LGA775 GIGABYTE GA-EP43-S3L (rev. 1.0) Intel P43 Express LGA775 GIGABYTE GA-EP45-DS4P (rev. 1.0) Intel P45 Express LGA775 GIGABYTE GA-EP45-UD3LR (rev. 1.0) Intel P45 Express LGA775 GIGABYTE GA-EP45-UD3P (rev. 1.1) Intel P45 Express LGA775 GIGABYTE GA-EP45-UD3R (rev. 1.1) Intel P45 Express LGA775 GIGABYTE GA-EX58-DS4 (rev. 1.0) Intel X58 Express LGA1366 GIGABYTE GA-G31M-ES2L (rev 2.x) Intel G31 Express LGA775 GIGABYTE GA-G33-DS3R Intel G33 Express LGA775 GIGABYTE GA-K8N Pro nForce 3 150 Socket 754 GIGABYTE GA-K8N51PVMT-9 GeForce 6150/430 Socket 939 GIGABYTE GA-K8NF-9 nForce 4 4X Socket 939 GIGABYTE GA-K8VT800 VIA K8T800 Socket 754 GIGABYTE GA-M61P-S3 (rev. 1.0) nForce 430 AM2 GIGABYTE GA-MA69G-S3H (rev. 1.0) AMD-690G AM2 GIGABYTE GA-MA69VM-S2 (rev. 1.0) AMD-690V AM2 GIGABYTE GA-MA78GM-S2H (rev.1.0) AMD-780G AM2 GIGABYTE GA-MA790FX-DQ6 (rev. 1.0) AMD-790FX AM2 GIGABYTE GA-P35-DS3L (rev. 2.0) Intel P35 LGA775 GIGABYTE GA-P35-DS4 (rev. 1.1) Intel P35 Express LGA775 GIGABYTE GA-P35C-DS3R (Rev. 1.x) Intel P35 Express LGA775 GIGABYTE GA-X38-DQ6 Intel X38 Express LGA775 GIGABYTE GA-X38-DS4 Intel X38 Express LGA775 GIGABYTE GA-X48-DQ6 Intel X48 LGA775 GIGABYTE GA-X48-DS5 Intel X48 LGA775 There are 45 MOTHERBOARDs listed here.