From what I know, Primus is also a deity, or at least there is a worshiper of one. Going to assume I'm getting my info from a canonical source... Also, Brohamut from what I can remember is simply Bahamut, only an older long lost version of worship.
I cannot believe that i forgot my favorite deity, the best deity in the history of D&D: Corellon Larethian of the Elves! Corellon was the patron deity of Fallowfield, the place they tried to warn about Yeenoghu's approach.
Y'know, I just gave the Eveningshire episodes another listen (for fan-writing purposes), and I'm not so sure the Glow Cloud exactly counts. It's referenced multiple times as being tied to magic, not divinity.
Ah! I'm re-listening to Episode 100, and I may have found another. Not sure if this counts as a deity, but there appears to be something called "The Guest Star" that grants power to certain characters. Probably a stretch, but I found it interesting.