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 MSI that can change fan speeds Manufacturer Model Chipset CPU Notes MSI 865PE Neo2-LS Intel 865PE Socket 478 MSI MS6163 v2.0 (6163 Pro) Intel BX Slot 1 MSI MS6199 VA VIA Apollo Pro 133 Slot 1 MSI MS6337 (815E Pro) Intel 815E FC-PGA MSI MS6337 v5.x (815 EPT Pro) Intel 815EP B-step FC-PGA MSI MS6351 Intel 815E FC-PGA MSI MS6366 Pro266 Master VIA Apollo Pro 266 FC-PGA more... MSI MS6373 K7N420 Pro nForce 420D Socket A more... MSI MS6380 (K7T266 Pro) VIA VT8633 Socket A MSI MS6380 v2.0 (K7T266 Pro2) VIA KT266A Socket A MSI MS6382 VIA KT266 Socket A MSI MS6385 Intel 850 Socket 423 MSI MS6398 (845 Ultra-ARU) Intel 845 Socket 478 more... MSI MS6398E v1.0 (845E Max2-BLR) Intel 845E Socket 478 more... MSI MS6507 Intel 845 Socket 478 MSI MS6528 (845 Pro2-R) Intel 845 Socket 478 MSI MS6528 (845 Pro2LE) Intel 845 Socket 478 MSI MS6533EG-LM SiS651 Socket 478 MSI MS6545 (850 Pro5) Intel 850 Socket 478 MSI MS6557 Intel 845GL Socket 478 MSI MS6570E (K7N2 Delta2 Platinum) nForce 2 Ultra Socket A MSI MS6585 v5.x (648 Max-V) SiS648 Socket 478 MSI MS6590 (KT6 Delta-FISR) VIA KT600 Socket A MSI MS6702 (K8T Neo-FIS2R) VIA K8T800 Socket 754 MSI MS6702E (K8T Neo2-FIR) VIA K8T800Pro Socket 939 MSI MS6704 (845PE Max2-FIR) Intel 845PE Socket 478 MSI MS6728 (865PE Neo2-FIS2R) Intel 865PE Socket 478 MSI MS6743 (865GM2-LS) Intel 865G Socket 478 MSI MS6758 (875P Neo-FIS2R) Intel 875P Socket 478 MSI MS6758 (875P Neo-LSR) Intel 875P Socket 478 MSI MS7025 (K8N Neo2 Platinum) nForce 3 Ultra Socket 939 MSI MS7030 (K8N Neo Platinum) nForce 3 250Gb Socket 754 MSI MS7047 (KT880 Delta Series) VIA KT880 Socket A MSI MS7051G (K7N2GM2-LSR) nForce2 Socket A MSI MS7053 (925X Neo Platinum) Intel 925X LGA775 MSI MS7071 (PM8M2-V) VIA P4M800 LGA775 MSI MS7093 (RS480M2-IL) ATI Radeon XPRESS 200 Socket 939 MSI MS7100 (K8N Diamond) nForce 4 SLI Socket 939 MSI MS7125 (K8N Neo4 Platinum) nForce 4 Ultra Socket 939 MSI MS7142 (K8MM-V) VIA K8M800-CE Socket 754 MSI MS7176 (945P Neo-F) Intel 945P LGA775 MSI MS7184 (AmethystM) ATI RS482 Socket 939 MSI MS7191 (RS482M4-ILD) ATI RS482 Socket 939 MSI MS7207PV (K8NGM2-FID) nForce 430 Socket 939 MSI MS7225 (Nash-GL8E) GeForce 6150 LE AM2 MSI MS7238 (MSI P965 Platinum) Intel P965 LGA775 MSI MS7250 (K9N Platinum) nForce 570 Ultra AM2 MSI MS7345 (P35 Neo2-FR/FIR) Intel P35 LGA775 MSI MS7510 (P7N Diamond) nForce 780i SLI LGA775 MSI MS7529 (G31M3-L V2 Intel G31 LGA775 MSI MS7576 (790GX-G65) AMD-790GX AM3 MSI MS7581 (P55-GD80) Intel P55 LGA1156 MSI MS7599 (870S-G54) AMD-870 AM3 MSI MS7640 (890FXA-GD70) AMD RD890 AM3 MSI MS7681 (P67A-GD65) Intel P67 LGA1155 MSI MS9105 (Pro266TD Master) VIA Apollo Pro 266T Dual FC-PGA MSI MS9130 (K8T Master2 FAR) VIA K8T800 Dual Socket 940 MSI Mega 865 Intel 865G Socket 478 MSI Z97 GAMING 3 Intel Z97 Express LGA1150 There are 59 MOTHERBOARDs listed here.