At the moment I'm guessing it's Megaton, not that I know how many people are still playing it. IIRC you can still use the original duke 3d in dosbox, and of course there's x/hduke around.
As for me personally, I'm holding out for eduke32. On top of all the minor improvements and conveniences, I imagine reduced lag, no loss of sync, and in-game joining are going to be huge improvments. Oh, and you also don't need to share maps and other files beforehand; only the host needs to have the files.
Another good thing about eduke32 multiplayer is all the mods you can have. Imagine playing WGR2 or AMC TC over coop, as well as finally being able to play some of the AMC TC's multiplayer modes. Plus any other multiplayer-specific mods that may come out.
If only we knew for sure progress is being made on it.