Best DOOM engine source port?

I use doomsday

GZDoom/Zdoom for single-player, Zandronum for multiplayer. The other ports cannot hold a candle to those.

Risen3D is really slick and worth a try.

GZDoom, without any contest. Why? Because I've been playing Doom for 15 years and I tried every single port that came out and GZDoom is the most feature-rich port currently out there, than can both be made to look like a more modern game OR be made to look and feel as vanilla as you want it. It's also the most moddable and the majority of the hot popular Doom mods use it.

I like ZDoom for absolutely no reason at all
maybe because its name is shortest and easiest to remember

ZDoom & GZDoom because they have amazing editing features, I messed around with them a few months ago made some custom weapons for Doom: http://www.youtube.com/watch?v=OoVtyO8S2cM

Wouldn't be that hard to make complete mods if you have the time and patience.