Zdoom doesnt have opengl unless you use Zdoomgl. Jdoom has scripting abilities already, you can do almost everything that you can do in Zdoom. Jdoom has lens flares, 3d models (good ones) Really cool smoke trails, glowing water, particles such as blood and fire clouds, Smooth model movement, New Hud Weapons, awesome lighting, Surround sound support, Mp3 support, and of course all of the basic stuff (auto aim off, crosshair, new hud, jumping, shortcut keys, etc.)
There is also pain skins for the monsters. The more you shoot them, the more bloody they get. Not to mention that the Zombies have several different faces like in Unreal Tournament.
Someone said that Zdoom is always getting better? They hardly ever update... Sky Jake is working on Jdoom all year around and constantly releasing new versions. The only better thing I can see about Zdoom is just a few extra scripting options, and that's it. Everything else looks 10x better in Jdoom. Infact, I am always in touch with Sky Jake, and he plans on making the next Jdoom support up to 85 FPS. It will also contain lots and lots of other good stuff.