Disclaimer: The author does not condone animal abuse in any way, and no penguins were harmed during the researching of this article.
It occurs to me, that the particular shape of the family of flightless birds, the penguin family, lends itself quite well to incorporation into numerous projectile weapon systems. The feathers of most penguins are sleek and smooth, highly aerodynamic, and each bird comes with a built-in stabilising device by way of their flippers/wings. In this respect they much resemble the armour-piercing shotgun ammunition known as a sabot round.
Penguins come in numerous sizes, roughly akin to the calibre of the desired projectile weapon. For example, a small, man-portable weapon could be constructed on a similar scale to the modern bazooka, the barrel of which would be an ideal size for the expulsion of Adelie penguins. The large (compared to a bullet) size of the Adelie would make this a formidable anti-infantry weapon, as few personal armours could offer protection against such a heavy projectile.
Further, at the other end of the scale, it would be possible to craft an enormous artillery piece, outweighing even the largest explosive cannons, built to accommodate the vast bulk of the Emperor penguin. Such a weapon would be of primary use against buildings and enemy tanks, as well as demoralising the enemy's ground troops. Soldiers are hardened against explosions and incoming shells, but a man's heart would soon quail if his base of operations were suddenly awash with penguin gore and entrails.
The sizes between these two extremes could cover vehicle-mounted weaponry, and the application of possible penguin-mortars. The major concern is storage of ammunition, and has led me to believe that frozen penguins would be the best idea. These could be thawed-out on site for use against some targets, or left frozen for a devastating effect on groups of infantry. Although it is theoretically possible to fire live penquins, the resultant death of the bird (and the possible decrease in accuracy) in the firing process makes this a somewhat unnecessary step.
The method by which the penguins are expelled requires the most thought, however. Conventional explosives cannot be used, unless you intend to create a penguin shotgun, spraying shredded flesh and bone over a short distance. A method akin to air rifles is more likely - a short, sharp expulsion of some form of gas. Let us not forget also the advances in air delivery of payloads, and a B-52 Bomber would likely be able to carry an enormous number of all sizes of penguins, both frozen, thawed and still live and kicking. These could be dropped from great heights, and used to carpet-bomb a wide area.
In conclusion, it is highly possible for penguin-based weaponry to become a staple of modern warfare, if necessary steps are taken to train the armed forces in the tactical usage of said weapons.
PS - Dont miss the next installment in the series, 'Cleaning your penguin-cannon, those pesky bits of beak...'