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 TYAN that can change fan speeds Manufacturer Model Chipset CPU Notes TYAN Tempest i5000XT (S2696) Intel 5000X Dual LGA771 TYAN Thunder K7 (S2462) AMD-760 MP Dual Socket A more... TYAN Thunder K7X AMD-760 MPX Dual Socket A TYAN Thunder K8W (S2885) AMD8111+AMD8131 Dual Socket 940 TYAN Thunder K8WE (S2895) nForce Pro 2200 (CK804) Dual Socket 940 TYAN Thunder i7505 (S2665) Intel E7505 Dual XEON TYAN Thunder i860 Intel 860 Dual XEON more... TYAN Tiger MP (S2460) AMD-760 MP Dual Socket A more... There are 8 MOTHERBOARDs listed here.