Bluestar's Prophecy is probably my most favorite book. It made me cry so. much. and I guess I just really like emotionally draining books? The plot was a lot different than what I was used to with the rest of the Warriors books, too. I also really love origin stories, and seeing all my favorite characters from the original series was like a second Christmas to me. Plus, like Dawnwing pointed out, it had a lot of original-arc-feel to it.
Other than that, I think Forest of Secrets and The Darkest Hour are tied for my second favorite books. They had so much plot in them that I found them both especially hard to put down.