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 SHUTTLE that can change fan speeds Manufacturer Model Chipset CPU Notes SHUTTLE AB60/N Intel 865PE Socket 478 SHUTTLE AV40 VIA P4X266 Socket 478 SHUTTLE FB81 Intel 915G LGA775 SHUTTLE FD31 Intel 945G LGA775 SHUTTLE FN41 nForce2 Socket A SHUTTLE FN45 nForce 2 Ultra Socket A SHUTTLE FS31 SiS662 LGA775 SHUTTLE FS50 SiS650 Socket 478 SHUTTLE FS51 SiS651 Socket 478 SHUTTLE FX41 VIA KM266 Socket A SHUTTLE SB51G Intel 845GE Socket 478 SHUTTLE SB61G2V3 Intel 865G Socket 478 SHUTTLE SB62G2 Intel 865G Socket 478 SHUTTLE SB75G2 Intel 875P Socket 478 SHUTTLE SN25P nForce 4 Ultra Socket 939 SHUTTLE SN26P nForce 4 SLI Socket 939 SHUTTLE SN41G2 nForce2 Socket A SHUTTLE SN85G4 nForce 3 150 Socket 754 SHUTTLE SN85G4V2 nForce 3 150 Socket 754 SHUTTLE SN85G4V3 nForce 3 150 Socket 754 SHUTTLE SN95G5 nForce 3 250Gb Socket 939 SHUTTLE SN95G5V2 nForce 3 Ultra Socket 939 SHUTTLE SP35P2 Pro (Prima Series) Intel P35 Express LGA775 SHUTTLE SS51G SiS651 Socket 478 SHUTTLE XPC RefleXion Intel 865G Socket 478 SHUTTLE Zen (ST62K) XPC ATI Radeon 9100 IGP Socket 478 There are 26 MOTHERBOARDs listed here.