In a map released before the game itself, two small islands can be seen in the upper right corner that are not in the final game. It's not known what these islands were or why they were removed.
Contributed by Mass Distraction
A hot air balloon is hidden at the coordinates X:7348 Y:16140. If the player shoots off all of the sandbags then activates the burner multiple times it will start flying. There is no way to control which direction it flies in and it's not possible to do a base jump off of it.
Contributed by EpicNoah15
In a tower located at the coordinates X:4245m; Y:25980m is weapon called the Bubble Blaster. As the name implies, this joke weapon shoots harmless bubbles. However, it acts as a real gun, causing civilians to run away and you gaining heat if you shoot it at the police.
Contributed by TheShadedMaster
Near the coordinates X:21898 Y:20254 is a secret message reading "Banana Fail", written in bananas.
Contributed by DeerBoarDude
There's an island located north west which pays homage to the television series "Lost". Whatever vehicle that you drive there will spontaneously explode, and on the island you'll find, close to the beach, a crashed plane, presumably the Oceanic 815, with the word "Search" scribed on the beach. Heading east down the southern coast, you'll come across the lost hatch and on the upper half of the island, north of a tower, you'll come across a soldier who makes an ominous clicking sound with clouds of black smoke following him, a reference to the smoke monster.
Contributed by KnowledgeBase
The map for Just Cause 2 is around 400 square miles. To put that into perspective the map is just over 133 times larger than the map in Grand Theft Auto 3, which is only 3 square miles.
Contributed by thescottishgamer