First of all its good that you realize that this is something you need to check with your players first. There will be many who will not be interested in exploring such themes
We also need to further define our categories here. Prejudice in settings not whole based on reality comes in two flavors
A) Real world prejudice. Every type of prejudice based on a characteristic found in the real world is on the category. Things like prejudiced based on gender sexuality real nationalities etc
B) Fantasy prejudice. Every type of prejudice based on a characteristic not found in the real world. Things like prejudice based on Fantasy races, being able to cast spells, fantasy nationalities etc
This distinction is extremely important because the first type is much much harder to present in a game context correctly (in some cases its basically impossible) and many players will not want to deal with it, and a very significant subset who have personally experienced it will rightfully have an extremely negative reaction to it
Never use this without explicit player buy in, and make it clear that they should inform you if they are uncomfortable so you can dial it down.
Now the second type is usually much more palatable and is often presented in many games and settings as a part of the world requiring no player buy in many cases. Ofc not all forms of it are the same. Prejudice against spellcasters vs prejudice based on how you look (the tiefling example) is fundamentally different. IF you are going to explore the theme in depth for the first case, or at all for the second, ask for player buy in/inform them of how the world treats em before making characters. If everyone in your setting hates tieflings, just tell that to the players, so that only a person interested in having that experience makes one and so on and so forth
Now for how to roleplay this
My answer here will focus on the second category. If you want to gather info for the first, simply look into how such prejudice manifests now or how it was historically applied and go from there
Firstly for fantasy races.
A society that loathes a specific race will have that race in lower regard. Expect to see them living in ghettos, having lower paying job with little social capital, and the ones who have important and influential positions are better than average to be able to overcome the roadblocks and discrimination, as well as treated with contempt and as an aberration. Its often likely that there will be less of them in such a society
For example in the first book of the rune lords pathfinder campaign in the first city there is only a single half orc and he is the garbage man. This tells you a lot about how half orcs are treated there
Prejudiced Npcs should put roadblocks to the pcs progress, refuse or think twice about associating with them or asking them for help, talk about them behind their backs, spread misinformation and slander about and doubt their achievements and capabilities. They usually will not admit to doing this on purpose and if confronted make up excuses and then proceed to behave even worse
If you want to go more extreme, that moves us to the realm of pogroms, denying pcs of said race (and anyone who is their comrade or friend)access to goods and services, lack of rights etc. depending on the extend of the prejudice expect npcs to be hostile to outright murderous. Its perfectly likely for a guard to attack the tiefling pc in a place where tieflings are considered little better than devils themselves, while a normal citizen or peasant would either retreat and call the guard or literally try to form a murderous mob, unless they are too afraid of the pc
Then lets talk about classes and spellcasting.
Its often that fantasy settings include this type of prejudice. For many its one of the main things about them, such as dark sun
Usually this manifests as prejudice either for or against magic. In dragon age all wizards are locked up in towers, abused and used as chattel. In the netheril empire in forgotten realms non spellcasters were second class citizens
Depending on the views on why said trait is bad, npcs will have a varied gamut of reactions. If the idea is that magic is powerful and dangerous they will try to not anger the pc and simultaneously find a way to get rid of them and escape the situation
If the idea is that magic makes someone weak, expect npcs to take spellcasting pcs less seriously, test their power, make biting remarks about "the wizard that cant even carry a bundle of firewood" or deny them access to culturally significant events on the grounds they are unproven and unsuitable
Prejudice based on fantasy nationality doesnt really differ from prejudice based on real life nationality ( so same as my point about category A previously). Because of that it can often be equally off-putting to players and very often carries with it other real life prejudice such as racism. Another thing to consider is how is that in many settings certain fantasy nationalities are based on real ones. For example, you brought up shadowrun. Sure the geopolitical environment is different, but prejudice against someone from UCAS is almost indistinguishable for prejudice against an American. In other cases fantasy nations are stand ins for real nations and cultures, so for example prejudice in the forgotten realms against someone who is Su is very close to prejudice against someone who is chinese. Ofc the basis is usually on past snapshots of said nations and cultures, but it is nevertheless often indistinguishable from historical prejudice against said nations and cultures, and some elements from 500 years ago haven't really changed today
so examine how close the nationality in question is to real ones. the closer it is to real nationalities the closer it is to category A
Oh and remember that elements from one prejudice often come at play in a different one. Excluding someone from culturally important events isn't only at play in case they are a spellcaster, its perfectly likely that they might be refused entry in a ritual because that ritual is "not for horned bastards like yourselves"