I use large Ziploc bags to stow my maps in the driver's-side cubby. All manuals and registration documents go in the glove compartment, also in Ziplock bags.
I don't live in an area that has tolls roads, but I have family that does, an empty pill bottle to keep change handy is a great thing to have.
In the backseat, use an organizer for toys, ice scrapers, and umbrellas.
A plastic tote is great in the trunk for emergency car supplies like jumper cables and flares.
Voila! Your car is now neat and uncluttered!