Which OS are you targetting? And which video card type?
Big choice is older AGP 8x or PCIe 1.0 for video. The PCIe chipsets were never designed for So754, but because the Athlon64 CPUs use HyperTransport to link to chipset, there's nothing stopping a motherboard vendor from using a chipset designed for So393 or later.
Keeping with AGP, you have a limited number of choices, as it was a short-lived platform. Basically it's nVidia nForce3 and its derivatives vs SiS 755, Via K8T800, ULi M1689. Generally I'd say nVidia nForce3-250 - but problem is that support for that was dropped by nVidia with Vista, so it works fine with XP and older, or indeed newer Linux distros, but it's a dysfunctional wreck with Windows Vista or later. Similarly, nVidia dropped support for ULi after taking them over, so no late driver support there. If you want to run them, go with Via. However none seem to have full drivers past Vista, which means big problems without specific AGP GART.
Lots of choices, mainly the nForce4 family and ATi Radeon Express 200 family and the ULi M169x-chipsets. With all these options driver support also dwindles to nothing past Vista, difference is that without AGP to worry about default OS drivers work much better. Personally I really like the ULi chipsets, but you'll only find ULi PCIe chipsets for So754 on obscure Asrock boards.