In the Dune series there are several mentions of the Orange Catholic Bible and quotations from it. But it looks like the book from the long forgotten past. Are there any mentions of major functioning religious organizations? By major I mean bigger then local planetary / solar system sects.
There is an official quasi-religion in the Imperium that forbids building a machine in the likeness of a human mind, whose doctrine is recorded in the Orange Catholic Bible. However, IIRC, there is no official religious organization a la the Catholic Church attached to it. Correct me if I am wrong, but it would seem that the ban on creating thinking machines is enforced by the Emperor.
On the other hand, the Tleilaxu have their own belief system, which can be considered a religion. And the Bene Gesserit also function as a religious order. Then, of course, there is the Fremen religion, centered around water and the sandworms. However, that is limited to one planet.
Jews are still around, keeping a low profile, but with their beliefs and practices essentially unchanged (see. "Chapterhouse: Dune").
There is also a blend of Buddhism and Islam, aptly named the Buddhislamic religion. It is given more attention in the prequels by Brian Herbert. Naturally, there are two branches: Zen-sunni an Zen-shiite. :)
To second the previous answer there is a strong hold of Jewish people throughout the Dune universe but what is most common to find are Buddislamists, Islam and Zensunni (which is part of Buddislamist). LINK
The Buddislamic faith was a broad, high-level belief system and cultural tradition that evolved through the joining of two ancient religions of Old Earth: Zen Buddhism and Islam. And according to the same source: "The Zensunni subgroup was historically the most commonly practiced."
I also remember that Azhar Book, which predates OCB, was developed by Bene Gesserit to gather all different faiths works into one consolidated body of work. I can only assume/suppose that it would have gotten "bible" rank.
There are a number of major religions, such as "zensunni" and "buddhislamic"
Having just read the appendix on religion in the original Dune, The Orange Catholic Bible was the work of the C.E.T. (Communion of Ecumenical Translators). It was written in the aftermath of the Butlerian Jihad (the war that rid the human race of computers). The C.E.T. was made up of representatives of all major religions (that is, religions with more than one million adherents).
The first document put out by the C.E.T. basically stated a unified declaration that they had agreed on but one thing - that no religion should have a theology that proposed that they were the one true religion to the exclusion of all others.
The OC Bible took years and years to complete and a number of the members of the C.E.T. needed to be replaced during its compilation as they died of various causes.
The OC Bible was released with a companion piece (commentaries basically) that turned out to be more influential than the actual OC Bible. Many religions rejected the OC Bible and it's now more studied as a historical document and philosophical text by people of influence in the galaxy than being the basis of any particular religion. And the Dune universe is full of religions (which, one would assume, have places of worship). Many of those religions are combinations of current Earth religions.
Muad'dib's religion is based on an extension of the Zensunni religion, which is a combination of Zen Buddhism and Sunni Islam. Note that the Missiona Protectiva (religious arm of the Bene Gesserit) has manipulated and planted many of these religions on strategically important worlds. The Fremen religion incorporates several Missiona Protectiva components - Reverend Mothers and the legend of the Lisan Al-Gaib (the voice from another world) and others. The MP did this to aid future Bene Gesserits in their hour of need.
Faiths specifically mentioned specifically include the Zensunni, the Buddislamics, the Jews, and the Christians, and the Bene Tleilax¹. Following the Butlerian Jihad, it would seem they all agreed to the civil stricture banning the making of machines in the likeness of the mind of a man. We have also the variant Zensunni rituals of the Fremen, and these take place in ritual spaces.
We also see the Fish Speakers - and they have actual churches. They are, however, a creation of Alia.
We should note that the Orange Catholic Bible quotes include some books from the modern bible, some from islamic suras, and some from other sources. It's syncretic. It also seems widely used, but not core to any faith presented.
Likewise, we see a general sense of lack of religious faith in the Atreides, Harkonnen, Corrino, and Richese houses. They all are aware of it, but come across as highly secularized themselves. Paul is well prepared to make use of religion as a tool; how much of this is due to the Bene Gesserit training, how much is due to having access to Bene Gesserit Other Memory, and how much is simply being raised an Imperial Nobleman is entirely unclear.
¹: Who are a perverse form of quasi-Islamic faith. They are not Muslims as we know them, but they are derived from Islam. We can presume them to be separate from the buddislamics and Zensunni.