Well, it depends on the time and place. Javelins were extremely common in Ireland and the Scottish Highlands/Western Isles (which shared significant cultural and linguistic links through the medieval period), and were one of the main weapons mentioned in nearly all historical records of warfare in these regions. For example, consider the following "arming of the hero" sequence from the Caithréim Thoirdhealbhaigh ("The Triumphs of Turlough," Turlough being the name of the chief protagonist), an early fifteenth-century history of the fourteenth-century war between two competing branches of the Ua Briain clan in Thomond (northern Munster, mostly modern County Clare by this point), and their English allies/opponents (it changed relatively often).

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Over the mail's upper part went a fine-textured white tippet of proof. He set on him a strong-plated conical helmet; took to him a broad sword, deeply fluted, having golden cross-hilt and tracery-embellished scabbard, which he girded to his side. In his right he took the handy dart, to hurl among the enemy; in his left he grasped the thickshafted solid-riveted great spear that abode with him, to bore with and to push.

"Dart" in this passage refers to a javelin or throwing spear. Later on in this same passage, the author describes how the two sides in a battle exchange javelins and slingstones before charging into melee:

On either hand continually they poured their darts into each other, sent the eager deadly javelins whistling on their way through shield and mail, and from their stone-propellers mutually a quivering cloud issued to fall in rain upon their heads and helmets, on their crests and weapons.

Similarly, in the eleventh century prose epic Caithréim Cellachain Chaisil, there are more references to the use of throwing spears before beginning the charge into melee.

However, when their youths, their champions and their
proud, haughty folk came to the front of the battle to
throw their stones and slender arrows and pointed spears
from each side of the heroes, the ground of the plain
was left to the soldiers, and the battle-field to the heroes,
and the place of slaughter to the veterans.

Even within the sixteenth century, when the Irish began using guns in ever-increasing numbers, there are references to continued use of throwing spears, such as in John Dymmock's A Treatise of Ireland, wherein he describes a native form of light infantry, the kern (from the Irish word ceithern, which is typically translated as "warband" or even more generally, "soldier")

The kerne is a kinde of footeman, sleightly armed with a sworde, a targett of woode, or a bow and sheafe of arrows with barbed heades, or els 3 dartes, which they cast with a wonderfull facillity and nearnes

As far as we can tell, Irish warfare in the medieval era always included the use of throwing spears, typically alongside the use of the slingstone and, from at least the Viking Age onwards, the bow. Even into the early modern era, as evidenced by the testimony of Dymmock (and others, not the least of which includes some rather fine artistic renderings of sixteenth century Irish warriors by various artists), the use of the throwing spear persisted alongside the use of the gun.

In Spain, the use of the throwing spear persisted throughout the middle ages as well. Almugavars (also spelled almogavars, and elsewise) were a nearly identical sort of soldier to the Irish kern in terms of equipment and tactics, being described by Lady Goodenough in her footnotes to the Chronicle of Ramon Muntaner thusly:

His weapons consisted of a short spear or lance, easy to throw, and of three or four darts which he carried slung on his shoulder, as reserve ammunition.

This light infantry, armed with spears and throwing spears and apparently some sort of knife, was apparently well-regarded by medieval Spanish polities, and formed a large part of the Great Catalan Company, which campaigned in the Byzantine Empire in the early fourteenth century. Jinetes, a sort of light cavalry armed primarily with javelins (similar, again, to native Irish cavalry, which fought with javelins and thrusting spear, wielded overarm, when they were not dismounted and fighting as infantry), were also a regular feature in warfare on the Iberian peninsula.

So javelins/throwing spears were actually quite popular in different parts of Europe (the Gaelic areas of the British Isles, and the Iberian peninsula were by no means the only regions that saw use of the weapon, but they are the ones for which I have sources at hand), and they remained in use even though these areas were also exposed to (and made use of) other forms of ranged warfare, such as the longbow or crossbow.

Primary sources used:

Caithréim Thoirdhealbhaigh, by Sean Ruadhri mac Craith, Tr. Standish Hayes O'Grady

Caithréim Chellachain Chaisil , Anonymous, Tr. Alexander Brugge.

A Treatise of Ireland, by John Dymmok.

The Chronicle of Ramon Muntaner, by Ramon Muntaner, Tr. Lady Goodenough.

Secondary sources used:

"Irish warfare before 1100." Charles-Edwards, T.M. A Military History of Ireland, eds. Bartlett, Thomas and Keith Jeffrey. Cambridge UP, 1996.

"Irish and Anglo-Norman warfare in twelth-century Ireland." Flanagan, Marie Therese. A Military History of Ireland, eds. Bartlett, Thomas and Keith Jeffrey. Cambridge UP, 1996.

I can provide links to, and more detailed bibliographic information for, the above primary sources if necessary, as they are all rather elderly translations but conveniently archived on the internet for public consumption. I have other secondary sources available as well, particularly for Ireland. I am much less well-versed in medieval Iberian warfare, but I do have some available for that era/area as well.