I just installed my MSI RS480M2-IR last Wednesday. It's a terrific board loaded with features and it's been absolutely rock-solid stable while I've been putting it through the ringer for the last several days. I'm thrilled with the board so far and I'm looking forward to adding my X800XL PCI-E card whenever ATI decides to ship it. I've been using the Xpress 200 IGP in the mean time. It won't set any benchmark records, but it's still very impressive for an integrated graphics core.
I chose this board because I was upgrading from an Athlon XP 2400+. For you, jumping to Socket 939 doesn't make much sense unless you were going to upgrade your A64 2800+ anyway. Socket 939 is considered more "future-proof" right now, but replacing your socket 754 processor for no reason doesn't make any sense.
PCI-E isn't a good reason to jump to Socket 939. Nvidia's entire lineup except possibly the 6800 Ultra is available in AGP. The 6600GT actually benchmarks faster in AGP mode than it does in PCI-E in most cases. ATI will be shipping X800-series cards in AGP form factor soon as well.
Socket 754 is projected to be around as a "budget" platform for a long time to come. The Athlon 64 series is being moved over to Socket 939 but the Sempron series is being moved over to Socket 754. The ATI Radeon Xpress 200 chipset that my motherboard is based on is compatible with both Socket 754 and Socket 939 processors.
Somebody will make a Socket 754 PCI-E motherboard, and they will make a crapload of money both for OEMs and for aftermarket sales. If you have your eye on a particular PCI-E graphics card, I wouldn't throw out your Athlon 64 2800+ just yet. If you want to stay with AGP graphics, the video chipset you want is either available there or it most likely will be soon.
Bottome line? There's nothing magical about Socket 939 and there's nothing magical about PCI-E graphics cards. There won't be any AGP SLI motherboards anytime soon, but I don't believe there's anything stopping an Nvidia partner from making a Socket 754 SLI motherboard, either.
Upgrading is always fun, but take the marketing hype with a grain of salt, and don't be in too big of a hurry to throw out your Athlon 64 2800+ too soon.