This is such a hard choice... I just finished reading the Wheel of Time... and the last book was the best in the series... in fact one of the best books I've ever read. There's also 2 other great series' to round out my favorite fantasy trifecta.... The Lord of the Rings and A Song of Ice and Fire. Since it took me so flippin' long to finish WoT I can't properly guage where it stands against those other two so....
I'll go with my longtime favorite... (from before I became a fantasy nut)
The Visitation by Frank Peretti is about a small town in Washington that recieves a man claiming to be Jesus Christ. I love this book for its character development. When I read it there are parts of it that really grip me emotionally, both happy and sad. There are key flashbacks in the book dealing with the main character's past that shape the way he recieves the man claiming to be Jesus. A very good read. (Note... if you've seen the movie... "Don't judge a book by its movie!" It is TERRIBLE! The WORST book to film adaption I've ever seen. In fact, despite the fact its my favorite book I refuse to watch the movie, EVER! They wrecked pretty much everything I love about the book)