The Flower & Garden Festival is gorgeous! I love seeing all the topiaries and the butterfly garden, etc.
I also do love the Food & Wine Festival, but it's becoming less and less unique now. They basically have a small portion of the F&W at Epcot during F&G.
Still, F&W has some cool offerings during its run. Last year they had a Ghirardelli Chocolate Factory exhibit at the Festival Center, which was very interesting. I tried their liquid choclate, which was a chocolate lover's dream, but also diabetes in a cup. Let's just say it was "foodgasmic".
Anyway, both Festivals are a blast, and I can't really point out my favorite because they're both lots and lots of fun!