To riffle, pronounced with a short i sound, is to peruse something quickly, usually by flipping through the items. It can also be used for shuffling playing cards or flipping the pages of a book or stack of papers. Common synonyms are ruffle and shuffle.
A riffle is anything that causes water to ripple, either on a riverbed or in a machine, this is mostly in North America though. It can also be a group if ripples or the act of shuffling.
To rifle, pronounced with the long i sound, is to hurried go through an area with the intention of stealing. It is more than just shuffling things around, it is making a big mess with explicit criminal intentions.
Rifle is also a weapon and can be used as an adjective to describe a certain way of cutting spirals to make a bullet fly farther. As a verb, it can be used in sports to say the player kicked or hit the ball and it sped off like a bullet.
In short, riffle is to look through and rifle is to tear apart in order to steal. Note the spelling and pronunciation differences as well. These two words are very commonly confused, both in spelling and pronunciation.
Examples
And so I riffled through my notes folder on the computer to try to find something suitable. [The Huddersfield Daily Examiner]
Investigators say the burglars entered through the roof and rifled through the entire store, including the pharmacy and the office. [CBS Pittsburgh]