This episode has been called the best of season five by various sources, including the ratings on this site. Frankly, I find it to be entirely overrated. It lacks the emotional depth which drives great episodes like "Homer and Apu", the absurdity of Burns' actions in "Rosebud", the epic proportions and visual fantastication of "Deep Space Homer" and the history described by "Homer's Barbershop Quartet". Unlike the truly great episodes, it fails to describe a plot from multiple points of view or to narrate the lives of multiple characters; it all revolves around Bart. Disappointingly, unlike the other season-five episode about Bart, "Bart Gets Famous", "Cape Feare" fails even as a vessel for Bart-style humor, since most of the gags are about Sideshow Bob hurting himself in typically cartoonish ways.
In the end, that is the real failing of "Cape Feare": unlike the many great episodes of Simpsons history, this episode lacks the initiative to be anything more than a great cartoon.