I don't think there's really an easy answer. The EPoX board's positioning of its SATA ports seems to be a little more practical than the MSI K8N Neo2, which has 2 of its 4 native SATA ports right above the AGP slot (although the EPoX EP-9NDA3+'s SATA ports are right below the AGP slot and right next to the chipset). However, the EPoX board uses a Marvell PCI SATA controller for two of its four SATA ports, meaning EPoX didn't implement the full potential of the nForce3 Ultra MCP. I chose the K8N Neo2 because of the fact that it implements all 4 of its SATA ports using the native nForce3 Ultra SATA controller (thus, your system is not doing so much I/O off the PCI bus if you're using more than two SATA devices). I also chose the MSI board because there were no reviews of the EPoX EP-9NDA3+ at the time.
A couple of other things, if EPoX sticks to their tradition of providing highly overclockable boards, then you might be able to get higher memory voltages on the EPoX board than on the MSI board (the MSI board tops off at 2.85V, which really should be more than adequate). Also, some forum members (including me) had a little trouble using the SATA ports on the bottom of the MSI board when overclocking. So again, no easy answer.
Therefore, if you plan on doing some hardcore overclocking and you don't care about the PCI SATA controller, then you might want to go for the EPoX board. If you plan on eventually being able to use more than two SATA devices and doing some mild overclocking, you might want to go with the MSI board. If you haven't bought any of your components yet, you might also consider waiting for the nForce4 Ultra, which gives you PCI Express and SATA 3Gbps. There should be some of these boards up for sale within the next couple of months.
One last thing, I don't know if I'd even consider the Gigabyte board previously mentioned. The only thing that really separates it from the MSI and EPoX boards is its Firewire 800 controller, which is also a PCI controller. Since its running off the PCI bus, you won't get anywhere near 800 Mbps (probably more like regular Firewire 400). In addition, the Gigabyte board has a combination of the MSI and EPoX drawbacks. It features the same awkward SATA placement of the MSI K8N Neo2 and the PCI SATA controller of the EPoX board, not to mention it has the DPS fan in addition to the chipset fan (extra noise).