These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
First Installment Wins: The original is generally seen as being much creepier than the sequel due to the lighting, atmosphere and other horror elements. The fact that the Creeper is shown more in the sequel also kills the scary factor somewhat. There are also other factors that make the sequel seem more like a generic teen horror film than the previous film.
The fact that the murder church from the first was based on a real killer's hideout helps it to be based in reality and thus scarier.
One-Scene Wonder: The axe the Creeper uses to cut off Gideon's head is never seen again for the rest of the film or in the sequel, aside from its brief appearance as one of the weapons that landed on Trish's car after Car Fu'ing the Creeper. Also shown in the Creeper's hand on the third film's poster.
Sequelitis: The second film was not as well received as the first.
Ironically, the whole premise of The Creeper ("every 23 years, for 23 days, it feeds") was written to avert this very thing, which led to Jeepers Creepers 2 to be set days after the first. The third film, however, will be set 23 years later.
Squick: Many moments, but the Creeper pulling the tongue out of a decapitated head with his teeth definitely qualifies.
Surprisingly Improved Sequel: There are those who feel that the second, while less subtly spooky, was far more thrilling and entertaining. It helps that, while we see the Creeper more often, the fact that it strikes from the air and disappears just as quickly made it more frightening.
Why Don't You Just Destroy the Corpse?: Jack Sr. beats the Creeper at the end of the second film, but only because the Creeper had to hibernate right then. Jack is Genre Savvy enough to believe the story that he will wake up in another 23 years. Rather than do the sensible thing and try to destroy the corpse so utterly that any revival will be impossible, Jack nails the corpse in his barn as a tourist attraction and makes sure that he'll be there to strike it down when it wakes up. Even if it is dessicated as all hell, there's really no excuse for even giving the thing a remote chance of escaping capture when you have more than two decades to perform every conceivable form of torture and/or mutilation on a being you know for a fact cannot retaliate.
The Woobie: Darry and Jezelle from the first film, and Minxie, Rhonda, Bucky and Jack Sr. from the second film.