Catholicism is the best hands down if you have a monopoly over the cardinals. In 90% of my games I go Protestant, as the idea cost reduction is tasty, and I don't feel like getting into a click war for the curia.
The second best IMO is Shiite. That morale bonus can't be beat, and since Shiites are scarce, that holy war CB will be used a lot.
For Eastern religions, it's Shinto. Similar to Shiite minus the 100% heir chance and the dual slider. Too bad it's only for Japan, as the other eastern religions suck beyond measure.
In fact, after 1.4, even Animism, Shamanism, and Totenism have better bonuses than Buddhism and Confucianism. I just find that ridiculous. I'd rather have a Shamanist Dai Viet than a Buddhist one
My rankings are 1. Catholic/Protestant, 2. Shiite, 3. Shinto. Top 3