This is a great prank to pull on a significant other, family member, or roommate as you need access to their car keys. As with any prank this should be used in jest and you should be prepared to reveal your shenanigans before things go to far.

The object of the prank is to make it look like the marks car was broken into, i.e. a "broken" window.

Note: The pictures here are a dramatic reenactment. The last time I pulled this prank the window of opportunity came suddenly and was short so I didn't get any pictures. Because of that there is less glass shown then you probably want to use to be really convincing.

Step 1: Supplies

Here are the conditions you need to pull of the prank.

Access, possibly with their keys, to the marks car.
At least one of the windows needs to go all the way down. The further down into the door the window goes the longer the prank can be maintained.
Time alone with the marks car, as close to when they next use it as possible. 5 to 10 minutes should be sufficient.
A hidden lookout position. Great for filming reactions but also you will need to keep an eye on the car after you setup the prank as the window will be wide open.

Supplies:

Glass - I've used a sheet of glass from an old scanner bed. Some other sources include old window panes, glass jars, old picture frames, etc.
Hammer
Old towel

The requirements for the glass are:

It's clear. Brown bottles and lightbulbs won't work unless the windows on your marks car are brown.
It doesn't break into real tiny pieces. If you're a classy prankster you will help clean up the mess you make and leaving tiny glass shards in your friends car isn't good.

If you have access to broken safety glass you could use that. It would be much more realistic but the small pieces will be harder to clean up.

Step 2: Break the Glass

What makes this prank work for more than a few seconds is scattering broken glass around. Safely containing and breaking glass is fairly easy.

Lay your old towel out on a hard surface, concrete is great.
Place the glass to be broken in the center of the towel and wrap it up securely.
Go to town with the hammer. Don't go crazy, you don't want powder or pieces that are tiny, pieces from 1/2" to 2" will be fine.
Carefully unwrap the towel being careful not to spill any of the glass and pick out the useable pieces, properly disposing of the remaining glass.
Re-wrap the useable pieces in the towel and store in a box until the time of the prank is at hand.

Step 3: Execute the Prank

When all the conditions laid out earlier are met it's time to spring the prank.

Get in your mark's car and roll down the target window. I prefer the front passengers side.
Carefully arrange broken glass on the inside of the car. Spread glass on the seat and floor but don't just toss it in, you need to be able to pick it all up again later. Don't worry to much about the amount of glass being the same as an actual broken window, your mark won't be paying that close of attention.
Add small pieces of broken glass sticking out of the gap where the window goes down. This little detail really bumps up the realism and can keep the prank running a little longer.
For a little psychological twist rummage around in the glove compartment and center console, spilling things onto the floor and seat but DON'T take anything, especially if they have something valuable. It will confuse them and make them wonder what was taken and why it happened if nothing was taken. If you want to tip them off in a funny way you can actually place something in the car that wasn't there before. Make it subtle but puzzling.
Hightail it to your hiding spot and wait.
Let the mark believe the break-in as long as you can. I even helped my friend seal his broken window with plastic. Don't let your mark file a police report or a claim with their insurance but, if you can convince them, go with them to a repair shop to have a mechanic take a look at it. This is the best way to revel the prank if you can pull it off. Make sure the mechanic knows your mark was pranked and not intentionally wasting their time.

Once again remember pranks should be all in good fun. Don't push it to far or when your mark gets you back it will probably go beyond a simple prank and the next thing you know you're on youtube in handcuffs because your ex-mark placed open alcohol containers in your car and disconnected your tail lights to get you pulled over (not from personal experience, just an example of going too far so DO NOT DO THIS, IT WON'T BE FUNNY).
Have a safe and hilarious April Fools!