Don't show more than you have to
Unless you have a very good reason not to, keep appearances of the various supernatural creatures very rare. For example, in a VtM game you have, by default, an excellent reason to have lots of vampire NPCs because the PCs are vampires and the setting encourages them to find each other and interact. However, there is no such reason why ghosts, fairies or witches would be especially common or visible to the vampires.
Some form of "Masquerade" or policy of silence is a common trope for supernatural groups in this genre. That means that even if multiple sorts of creatures are present in a city, they will probably not notice each other unless a specific plot device is bringing them into contact.
The lone example
Sometimes, having just a single representative of a group appear can help reinforce the feeling of rarity. Sure, the party is used to werewolves and probably some of them believe in ghost stories. But they've never seen a real ghost until tonight!
An encounter like this lends more credence to all of the tales of "others" that abound. It tells the players that there really are lots of hidden things in this world. Because they only saw the one, it also tells them that these things are hard to find and they probably know very little about them.
Be careful not to overdo this. If you get to see one example of every creature type then "weird supernatural critters" start to feel common even if one particular species doesn't. One example of one or two (at most) things will do the trick.
Scare the mundanes
If supernaturals are rare, then most humans don't either know know about them or have never (knowingly) seen one in action. Have a human witness in a scene who can become terrified or dumbstruck at the sight of blatant supernatural power. Let this person's emotional reaction illustrate just how fantastical the monsters really are.
Compare and Contrast with Humans
Make humans plentiful. Chance encounters with supernaturals shouldn't happen much. Either the PCs are seeking one out, or being sought out. If you're just walking down the street it should be filled with regular human beings.
Show that the monsters are different. In something like VtM, this often means setting up a situation in which the PCs' vampirism sets them apart from humanity, often in a socially isolating way.
Interacting with a family with children who are sleepy from being out late at night. THe vampires cannot have kids, and probably see disproportionately few children due to their nocturnal habits.
A friendly mortal is injured in an accident, and the PCs are the nearest people. The NPC, bleeding and in pain, asks them for help. Portray the NPC sympathetically, and possibly introduce them earlier so they're already liked. Then, describe the person's blood in terms tantalizing terms. Watch you players' blood pools and time this so at least one PCs should need to check for frenzy when they try to be helpful.
If the PCs are human, show them examples of NPCs acting in ways that no same human would. This doesn't have to be outright villainy (but it can be in an us vs them story).
- Some human-form werewolves are having a civil chat with the PCs. When finished, they transform to go hunt a deer with their pack.