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 ABIT that can change fan speeds Manufacturer Model Chipset CPU Notes ABIT BD7 Intel 845 Socket 478 ABIT BD7 RAID Intel 845 Socket 478 ABIT BE6 Intel BX Slot 1 ABIT BE6-2 Intel BX Slot 1 ABIT BF6 Intel BX Slot 1 ABIT BL7 Intel 845 Socket 478 ABIT BP6 Intel BX Dual PPGA more... ABIT BW7 Intel 845 Socket 423 ABIT BX133-RAID Intel BX FC-PGA ABIT BX6r2 Intel BX Slot 1 ABIT DiGiDice Intel 865G Socket 478 ABIT IC7 Intel 875P Socket 478 ABIT IC7-G Intel 875 Socket 478 ABIT IC7-MAX3 Intel 875P Socket 478 ABIT IP-95 VIA P4M890 LGA775 ABIT IP35 Intel P35 Express LGA775 ABIT IS7 Intel 865PE Socket 478 ABIT IS7-E Intel 865PE Socket 478 ABIT IS7-G Intel 865PE Socket 478 ABIT KD7A VIA KT400A Socket A ABIT LG-95C Intel 945GC LGA775 ABIT NF7-M nForce2 Socket A ABIT NF7-S nForce2 Socket A ABIT NF8 nForce 3 250Gb Socket 754 ABIT NV7-133R nForce 415D Socket A ABIT NV7M nForce 420D Socket A ABIT SA6 Intel 815EP FC-PGA ABIT SA6R Intel 815EP FC-PGA ABIT SA7 SiS645DX Socket 478 ABIT SE6 Intel 815E FC-PGA ABIT SH6 Intel 815E Slot 1 ABIT SL6 Intel 815 FC-PGA ABIT ST6 Intel 815EP FC-PGA ABIT ST6R Intel 815EP FC-PGA ABIT TH7II-RAID Intel 850 Socket 478 ABIT VA-20 VIA KM400A Socket A ABIT ZM6 Intel ZX PPGA There are 37 MOTHERBOARDs listed here.