The preacher's pain (Situational Irony)
Although the preacher is reacting to his own pain when he pulls away from his daughter, he hurts his daughter who has lost her only other parent. Therefore even though he is hiding from pain, he is creating more of that which he hides from. His attempts to prevent pain in fact cause it, leading to situational irony.
Gloria Dump is a witch (Dramatic Irony)
When the town boys tell Opal that Gloria Dump is a witch who will eat her dog, the reader knows better than to believe them, both because 1) Winn-Dixie's instinct is never wrong and 2) witches aren't real.
Winn-Dixie hiding under the bed (Situational Irony)
Opal is terrified when Winn-Dixie goes missing, and she feels guilty for leaving Winn-Dixie out in the rain. She insists she and her father leave Gloria Dump's house in order to search for him in the rain. What Opal doesn't know is that Winn-Dixie had run into Gloria Dump's house out of fear, and he had been hiding under the bed the whole time.
The preacher and Winn-Dixie (Situational Irony)
Although the preacher is initially resistant to letting Opal keep Winn-Dixie, he learns to love the dog as much as his daughter. Something he had thought would be an inconvenience ended up being the biggest blessing in his and his daughter's lives.