There's a dichotomy between "good" Christianity and "bad" Christianity, a.k.a. the "they're not true Christians" according to the nicer Christians. It's clear that some of the "bad" Christians seem to belong to the same few denominations.
What is a "bad" Christian? In my view it's someone, or a group of someones, who use religion to justify hurting other people. When they hurt their own children, that multiplies my disgust.
Independent Fundamentalist Baptist Church (IFB)
These are the most extreme of the Baptists. They have their own colleges, (including Bob Jones "University") but because they are independent, a pastor can make up his or her own interpretation of scripture. Bruce Gerenscer, now an atheist blogger, used to be an IFB pastor. (See his guide to IFB-speak and his personal story)
I started with the IFB movement because it's timely: this Arizona pastor argued that gay men should be stoned to death, and went on a rant against a fellow IFB pastor who disagreed with him. If you aren't willing to kill gays, you are weak in his opinion. How long until his congregation starts killing people? (or one like him) How many other IFB pastors are preaching the same doctrine?
The IFB pastors have absolute theological power over their congregations, and they only answer to Gawd. Even though there are IFB colleges, there is no theological structure to rein in the pastors. The ministry often passes from father to son, risking a cult of personality and dynasty. There is also a culture of secrecy, like the Roman Catholic priesthood. Pastors find new jobs easily because their sex crimes are kept covered up.
Between the pastor's divine inspiration, the cult of personality, and the extremism of the theology, they are the one Protestant denomination to watch. Some megachurches are IFB, making their cultish influence even more sinister.
Some of their illustrious sexual predators & one evil enabler:
Jack Schaap in Indiana: a sexual predator who pastored in a church that had a long history of permitting sex abuse. He's now in prison, but his influence lives on in the sex abuse of other IFB jerks.
Bill Gothard, best known as a leader of the homeschooling movement... at least until his organization suffered financially and he was outed as a sexual predator. Although never married, he is an expert in marriage and his teachings form part of the Duggar family "values." This "quiverfull" movement victimized Andrea Yates
Chuck Phelps is best known for forcing a teenaged girl and her rapist to publicly confess in front of their IFB congregation. After that he found a temporary home for her out of state for her to have her baby and then give it up for adoption. After the sordid story became known (and widely known, thanks to a 20/20 episode), he was forced out of his position at Bob Jones University. You'd think he'd be out of the pastor business after that but no. He's the head pastor of a megachurch in Indianapolis. Perhaps God had the last word, though. His son & daughter-in-law died in a church bus crash. The driver was not charged despite excess speed being the cause of the crash. Who needs Heaven & Hell when there's Karma on the highway?
They are also physically abusive to children:
Not far from Jack Schaap's church, Fairhaven Baptist Academy in Indiana uses physical abuse to humiliate children: A CNN exposé on this school didn't seem to affect the pastor. He still works at the church and he is the chancellor of the associated (unaccredited) college.
This was one of many reform schools for girls, thanks to an evil genius named Lester Roloff. Mother Jones's exposé of a Missouri "school" reveals just as much abuse.
Bruce Gerenscer writes about New Bethany school in Louisiana (with lots of links).
There are many blogs and websites run by ex-members, both Christian & atheist. This site has a list of articles for further reading, if you have the stomach for it.
...so I vote them as the #1 most dangerous denomination because of their actual abuses and the potential for much much worse. Let's hope they don't start stoning gays to death, but could you put it past them?
edited to add: And then there's the "Faithful Word Baptist Church" which was founded by an anti-gay pastor who also hates Obama and wants him to die.
4/20/2015 edited to add: Franklin Graham, son of IFB pastor Billy Graham, has announced what basically amounts to an attempt to create a theocracy:
“America is in trouble. At 62 years of age, I’ve lived long enough to learn that neither the Democrats nor the Republicans can turn this country around; no political party or politician is the answer. The only hope for this country is Almighty God and His Son Jesus Christ. Next year I am planning to travel to all 50 states to conduct prayer rallies—we are calling this the Decision America Tour. I want to challenge Christians to boldly live out their faith and to pray for our nation and its leaders. I want to encourage Christians to get out and vote, and to cast their ballots for candidates who uphold biblical principles. I want to strongly urge Christians to run for public office at every level—local, state, and federal. We will not be endorsing any political candidates, but I will be proclaiming the truth of God’s Gospel in every state. More details will come later. I hope you will start praying with us now.”