There's a candy bar called Cuj-Oh's in the vending machine.
Norman's friend being called Neil may be a shout out to Neil Gaiman, given that he wrote the source material for Laika's previous success Coraline (as well as The Graveyard Book, which shares some similarities with ParaNorman).
Judge Hopkins is named for the title character of the Tigon horror film Witchfinder General.
When we physically first see Agatha, she's wearing ruby slippers.
Also, her name itself may be a reference to a certain Pokemon Trainer whose specialty was the Ghost type.
There are several shout-outs to Scooby-Doo, although, of course, they don't have a live dog:
The police officer uses the phrase; "Those meddling kids"
She even says "Jinkies" when they come across the mob.
For part of the movie they're driving around in a van like the Mystery Machine.
Salma, the smart one, could be a shout out to Velma, the smart one.
Confirmed by the commentary. And the reason they call Salma instead of bringing her along because that's what would happen in real life. The gang wouldn't bring Velma on the dangerous adventure, they'd call her whenever they needed information.