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 ECS that can change fan speeds Manufacturer Model Chipset CPU Notes ECS 661FX-M7 (V1.1) SiS661FX LGA775 ECS A535 SiS740 Socket A ECS Desknote A530 ALi M1535D+ Compact 474 ECS Desknote A531 ALi M1535D+ Compact 474 ECS Desknote A928 SiS650 Socket 478 ECS Desknote A929 SiS740 Socket A more... ECS G320 VIA CLE266 FC-PGA ECS G713 SiS746FX Socket A ECS K7VTA3 v1.x VIA KT266 Socket A ECS KV2 Extreme V1.0 VIA K8T800Pro Socket 939 ECS L7S7A2 SiS746 Socket A ECS N2U400-A (V1.0) nForce 2 Ultra Socket A ECS P4ITA Intel 850 Socket 423 more... ECS P4M800PRO-M (V1.0A) VIA P4M800Pro LGA775 ECS P6IPA-T Intel 815EP FC-PGA ECS RS400-A (V1.0) ATI RS400 LGA775 ECS RS480-M (1.0) ATI RS480 Socket 939 ECS nForce4-A939 nForce 4 Socket 939 There are 18 MOTHERBOARDs listed here.