Well, to be fair, it's hard to explore God in the framework given in Incarnations of Immortality. I quite enjoyed And Eternity, and Being a Green Mother is probably my third favorite of the series...the ones that I liked least were Wielding a Red Sword, mostly because I found it very difficult to relate to Mym's worldview, and With a Tangled Skien--for reasons I can't quite articulate.
Another good series of his was the Mode books (at least, Virtual Mode and Fractal Mode--the other two were somewhat of a let-down). Much like the Apprentice Adept series, those were an intriguing blend of sci-fi and fantasy, and some of his deepest characters. There are also some good things to be said about his Tarot series, but it's been awhile since I've read them.