Inspired by my own wondering why Bob is so fixated on Bart.
Snake had once asked Bob why he hated Bart Simpson so much, and Bob actually couldn't come up with a simple answer.
Why did he hate Bart so? Sure, he'd foiled Bob's plans, but only on their first three encounters, and to a lesser extent, that last time at Five Corners. It would have made more sense for him to hate Krusty, Cecil, or Lisa. After all, Krusty had started all of this; if Bob had never been on Krusty's show, he never would have been humiliated enough to frame him for robbery, and he never would have met Bart. Cecil had tried to kill Bob and Bart, who had saved each other from him. Lisa had helped to trick Bob into confessing electoral fraud, and she'd exposed Bob's hiding place in the Duff blimp, and gotten drunk in Italy and revealed his past to the villagers, and figured out that Bob had faked his death.
But Bob had, for the most part, buried the hatchet with Krusty once the clown had sincerely apologized on what would have been his last show. As for Cecil, it didn't feel right to want to kill his own brother; he wouldn't stoop to Cecil's level, and he felt a mild, lingering protectiveness over his little brother. Lisa may have been a child, but she was a smart child, if highly smug and self-righteous.
For a highly educated and well-spoken, if insane, man, it felt the worst to be bested by an underachieving and mouthy prankster. That was why he hated Bart Simpson the most.