As promised here's the results of my investigation of the motherboards I have or have had in the last few years with regards to their support for multiple floppy drives. I know this is notionally a 'software' forum, but it seemed the best place for this, if the admins disagree, then please feel free to move it. Also please feel free to make it sticky so that it is easier to find / add to.
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Motherboards know to support two floppy drives.
All boards also support High, Double and Single density unless stated
Boards tested by Phill HS / Prime unless otherwise stated.
Board Arch Notes
Gigabyte GA-71XE Athlon Slot A
Gigabyte GA-7ZX Athlon
Iwill KK266 Athlon
Iwill KK266-plus Athlon
Asus A7M266-D Athlon XP/MP
Asus A7V266E Athlon XP Supports 2 drives - cmjones01
Asus A7V8X-X Athlon XP Does not support 360K drives in BIOS.
Asus A7V600 Athlon XP Does not support 360K drives in BIOS.
Abit NF7-S Athlon XP
ASRock K7S41GX Athlon XP
ABIT AN8 Fatal1ty Athlon 64-939
Shuttle SN68SG2 Athlon 64-AM2 Needed BIOS modification to enable 2 drives / 5.25"
Shuttle SG22SG2 Athlon 64-AM2 Needed BIOS modification to enable 2 drives / 5.25"
Shuttle FS50v1.3 Pentium Native support for 2 drives & SD/DD/HD - Arcadian
Shuttle SB52G2 Pentium Native support for 2 drives & SD/DD/HD - IanB
Shuttle SB51G Pentium Native support for 2 drives & SD/DD/HD - IanB
Motheboards known **NOT** to support 2 floppies.
This may be lack of BIOS support or that the floppy disk controller only physically
supports a single drive.
Board Arch Notes
Intel D845GRG Pentium 4
Intel D845HV Pentium 4
Asus A8N-SLI series Athlon 64-939 FDC only supports 1 drive.
Asus M2N-SLI Delux Athlon 64-939 FDC only supports 1 drive.
MSI K8N Neo4-FDC Athlon 64-939 FDC only supports 1 drive.
Gigabyte M61PME-S2 Athlon 64-AM2+ FDC only supports 1 drive.
ASRock N68-GS Fx Athlon 64-AM3+ FDC only supports 1 drive.
Gigabyte GA-MA770 Athlon 64-AM3+
Edit: 2016-09-24, Added Shuttle SG22S2.
Edit: 2016-09-30, Added boards verified by Arcadian, cmjones01, IanB