My number one favorite tool to use for my Amigurumi's is a felting needle. it give the project a more finished look and I think it looks a lot better than hot glue. This is a great tutorial on how to use it.
My other favorite tool to use is a white puff paint pen. It puts the finishing touches on the eyes of amigurumi. I found it difficult to cut the felt small enough to make a difference. The pen gives just the right amount and makes everything pop.