It says in several books that the religions which always incorporated magic got a big boost. That means shamanic traditions like Native American Shamanism and neopagan religions like Wicca, Asatru or celtic Drudism. These religions now have a big following in the western world. The eastern religions like Taoism, Buddhism or Hinduism are also on the winning side of the Awakening and are in good shape. Shinto is of course going strong in Japan. After all, this is a cyberpunk setting
On a more serious note: Shinto fared well and this makes sense, since it's a shamanic religion focused on spirits.
For the Abrahamitic religions:
Islam still dominates the arab world and most (but not all) muslim schools declared magic a dangerous art. There is also the Islamic Renaissance Movement, which aims to reform Islam just like Luther did with Christianity. The Movement is pretty strong and could even become a new major school of Islam.
Catholicism lost many followers because it didn't adapt well to the sixth world (it banned magic and metahumans were seen as lost causes). After a while, a new pope (the old one died under suspicious circumstances) accepted magic as a gift from god and allowed it's use as long as it is used for good. He also classified metahumans as equal to humans. The church has since consolidated, but is still not as strong as before the awakening.
Protestant churches are very varied (as always), but most adapted pretty well. Many of them were more magic friendly than the catholic church.
Don't remember how Judaism and the orthodox christian churches developed exactly, but both are still around.
Atheism is also strong. While nobody can deny magic and spirits in Shadowrun, you can still deny that these beings have any moral superiority and deserve veneration. Many see magic as just another, although as of yet unexplained, part of the universe which can be understood by science. The scientific hermetic mages subscribe to this belief.
Bonus: It is VERY strongly implied that Scientology evolved into the Universal Brotherhood. This group evolved into a big insect spirit cabal and was utterly destroyed after this was discovered.
