Depends on how you want the encounter to go.
For Mind Flayers, if you want to more put your players on edge, use some of the fluff from Lords of Madness - have the players find a village that's completely empty, with no signs of struggle, except (if the pass the skill check) some unseen and alien footprints and bits of robe stuck to a nail, that kinda thing. Nothing that would give away who did it, merely that something else was here. Continue the mystery in the next village - people are going missing, and nobody sees what's happening. Maybe catch an errant person right as they're being fed - they don't see the mindflayer doing it, they just heard a "sickening, squishy, organic sound" and turn the corner to find a dead body with no telltale signs of death. Or maybe the Mind Flayer thralls attack the village to collect slaves - you don't see the flayers, just the underdark creatures kidnapping villagers, but (and again apply a skill check) your players discover that there's something wrong about them. Maybe they never speak, only occasionally drool and walk in a zombie like state. Maybe one breaks free of the mental control long enough to write "HELP ME" in large letters on the side of a building. You get the idea. Follow the thrall caravan and find a map to their village, and there you go - the players are in a collision course ith mind flayers, but potentially don't know that they ARE mind flayers - just that they're something evil, something alien, and something that effects creatures' minds.