Taxing them into the ground. You need to pay to move things, just like today. You have to buy a car, pay for the gas, put everything in the car, buy a new home, unload everything, and continue to pay rent/mortgage on your new place. You also had to pay to use your lord’s land resources - cutting wood, hunting, fishing, etc. It was a token amount usually, but it was there. You further had to pay for the lord’s baker to make your bread. You didn’t just have an oven in your house, they were communal, and operated by a professional baker. Usually you could mill for free though.
All of this mobility is far beyond the means of the poor in today’s free society, so considering you would have to literally buy your freedom (essentially buying the lease from the landowner, without a legal transfer of land ownership), you likely were not going to go anywhere as a serf. If a serf ran away, there were generally unspoken agreements that one landowner would return the serfs of another landowner, and would expect the same in return. Sort of like extradition treaties with the neighboring lords, particularly when they were related. Though the system where you could live in a city for a year existed, it was generally restricted to only those who were A) Close to such cities B) were generally unneeded in their lord’s manor anyway, and could hide for that long and C) already wealthy enough to afford to travel there and survive for said year.
Far more common than running or buying your freedom however, was to volunteer for the lord’s military. The military paid a healthy amount, and you could also work on the farm while not at war and earn extra money that way. Then it became much more likely for you to be able to buy A) Better weapons and armor, becoming a true knight in your lord’s retinue, eventually becoming a landowner yourself or B) Your freedom, allowing you to move to the city and become an artisan if you had a craft, or hire serfs of your own to work the land, while you contemplated expansion.
You could also legally buy the land from your lord if he were inclined to sell it, but because you’re still in his demesne, you still owe him taxes. That was far more common than outright serfdom in much of Europe. Serfdom as we think of it today was only particularly common in areas of France, Russia, and some parts of Germany and Britain depending on how big of an asshole the local lord was.
Power politics. You did it because he told you to, and if you didn’t, he was going to strip you of your right to work that land (read: your income), your possessions (your house, and any money you had stashed there), and in some of the more dastardly lordships, you were required to send at least one son to be a part of his military or the local clergy - essentially a hostage. Daughters would instead be required to work as handmaids, threadspinners, basket weavers, etc. in his Lordship’s castle/manor. Only an ass would up and leave his children to the mercy of a lord who’s a big enough dick to make you want to leave.
Also, technically they were never paid. They grew X amount of crops, and were allowed to keep some of it. Nitpicking perhaps, but it’s an important distinction - the lord didn’t owe you anything except protection and access to the clergy, and enough food to survive.
The courts were run by Jones’ manor holders. If he was a manor holder and had no other manors under his command, then the matter would be brought up in his lord’s court, where he would presumably not be allowed his normal place on the bench.
Except for Scandinavia, where the culture and demographic nature of the area made serfdom ill suited for use. They continued to use the Leidang into the high middle ages instead of organizing systems of serfdom (though they did experiment with serfdom in some areas, most notably areas of Denmark which had higher population densities, and closer connections with the Holy Roman Empire). Those experiments quickly tended to fail, because of the shortage of labor. It led to the serfs who did exist to rake in the dough.