They are bees, and along with the eagle they were the most important animal symbols of the Second as well as the First Empire.
Their history dates back to the earliest French kings. The 5th-century king Childeric I, father of Clovis and founder of the Merovinginan dynasty, was buried with around 300 golden bees that looked like this. These bees were the source of much fascination when the tomb was rediscovered in 1653.
Napoléon I, in search of a replacement for the monarchist fleur-de-lys, settled on the images of golden bees. He observed that bees "have something national about it: some were found at the tomb of Childeric, and this insect is the symbol of activity. The stars will be for me, the bees for the people." It's also hard to resist the reputation of diligent obedience before a leader that bees have. And so he had the draperies adorned with bees for his coronation at Notre-Dame in 1804, and many of his imperial robes were covered in bee motifs, such as here. Napoléon III adopted much of his uncle's imagery, including the bees, as you see on the standard.
From a vexillological standpoint, during the monarchy the royal standard looked something like this. Note that the flag is covered (in heraldic terms, semé) with fleurs-de-lys. Napoléon III did the same thing with the French tricolor, but instead of the monarchy's fleurs-de-lys, he chose the empire's bees.
