I have to say that Red Equinox, by Douglas Wynne, is probably one of the better Lovecraftian novels that I've read. It's not a particularly original one, but Lovecraftian horror usually isn't.
It uses the standard plot about a secret society who is plotting to release the Great Old Ones and bring about the destruction of humanity. This is a plot that H. P. L. himself used, so it's not all that original. Even the addition of a secret government agency tasked with stopping supernatural evil doesn't help, as that's been done so much it's rapidly becoming cliched.
I think what really set this story apart for me was the characterization. I don't know why, but I found myself genuinely caring about the characters, even to the point that when the protagonist was temporarily grabbed by the aforementioned secret government agency, I found myself getting angry on her behalf.
This is a book that I'd recommend to any fan of Lovecraftian horror.