This isn't something I've studied in any detail so I condone the deletion of this post in case it isn't quite up to the sub's standards, however, this has come up in my studies once.

When Nikephoros II Phokas invaded Crete in 960 CE he besieged the largest city on the island, Chandax. During Leo the Deacon's account of the siege he mentions the following,

"And now the general prepared yet another triumph on top of this new triumph. He ordered his men to cut off the heads of the fallen host, and to put them in leather satchels to carry them back to camp, and he promised to give a reward in silver to every man who carried a head. The army, especially the corps of Armenians, received this command gladly, and cut off the barbarian heads and put them in satchels.Then the general returned to camp by night. The next day, as soon as the sun rose above the horizon and began to climb toward the vault of heaven, Nikephoros ordered his men to impale some of the barbarian heads on spears and set them up in a row next to the wall that he had built, and to hurl the others at the town with stone-throwing machines. When the Cretans saw the line of spears and the heads impaled on them, and the heads that were hurled at the town and crushed against its battlements, and when they clearly recognized them as the heads of fellow countrymen and relatives, straightaway they were seized with horror and mental confusion, and were paralyzed at the piteous and unexpected sight.Then the lamentations of men and the wailing of women were heard, and the town took on the appearance of one that had been conquered, with everyone lamenting and bewailing his loved ones. But even so the town would not yet yield to the Romans and surrender; but confident in the strength of their town, they summoned up their courage and waited fully armed for the Roman assault, so that if anyone attacked they might defend themselves."

Not exact bodies but it seems heads may have been catapulted over the wall during the siege.

Source: The History of Leo the Deacon, Book I

There were certainly instances where invading armies would use dead bodies as siege missiles. I am not overly familiar with their use as an intimidation tactic but they certainly do come up when you look at the history of biological warfare prior to the modern era.

From the linked article on the siege of Thun l’Eveque (1340):

The duke caryed with hym out of Cambray and Doway, dyverse great engyns . . . and made them to be reared agayne the fortres, so these engyns dyd cast night and day great stones, the which bete downe the roffes of the chambers, halles, and towres, so that they within were fayne to kepe [to the] vautes and sellars . . . The ingens without dyd cast in deed horses, and beestes stynking, wherby they within had great[er] dystres thane with any other thynge, for the ayre was hote as in the myddes of somer: the stynke and ayre was so abomynable, that they consydred howe that finally they coude nat long endure

It should be noted that the primary function here seems to be to discomfit the defenders and not necessarily to employ biological warfare.

However, from the same article, the siege of Caffa (1346) is more well known and is potentially the source of the Black Death plague's entry into Europe:

But behold, the whole [Mongol] army was affected by a disease which overran the Tartars and killed thousands upon thousands every day. It was as though arrows were raining down from heaven to strike and crush the Tartars’ arrogance. All medical advice and attention was useless; the Tartars died as soon as the signs of disease appeared on their bodies: swellings in the armpit or groin caused by coagulating humours, followed by a putrid fever.

The dying Tartars, stunned and stupefied by the immensity of the disaster brought about by the disease, and realising that they had no hope of escape, lost interest in the siege. But they ordered corpses to be placed in catapults and lobbed into the city in the hope that the intolerable stench would kill everyone inside. What seemed like mountains of dead were thrown into the city, and the Christians could not hide or flee or escape from them, although they dumped as many of the bodies as they could in the sea. And soon the rotting corpses tainted the air and poisoned the water supply, and the stench was so overwhelming that hardly one in several thousand was in a position to flee the remains of the Tartar army.

The article goes on to say:

While it is nearly certain that refugees from Caffa contributed to the spread of plague, it is less certain that the plague within the walls of Caffa was the result of biological attack.

There are several other incidents cited in the article and it's worth a read in its entirety.

However, to answer your question, it's not clear if the practice of using corpses as siege ammunition was "common" but it certain was used to great effect in several instances.