Wikipedia lists the following churches as participating:
* The Protestant Church (the "big one", there are myriads of small protestant free churches, especially in southern Germany – none of which participates)
* The Catholic Church
* The Old Catholics
* "Free Religion Congregations" (a special group)
* The Unitarians
* The Jewish congregations
It also lists twenty-two churches that don't let the state collect money on their behalf, including the Methodists, the Salvation Army, Mormons, some Pentecostal church, Alevits, Muslims and so on).
That's deceptive. The tax form lists several churches that have decided to let the state collect their "membership dues". Many churches and denominations have declined to do so, and you won't find them on the tax form. You simply tick "none" if you're not a member of those specifically listed churches. And if you are, well, you owe that money to the church. You're free to leave that church.
Having tithes collected by the state is a breach in the separation of church and state (for historical reasons), but it's not like the churches have no choice.