In the Bloodsucker Village in So C a small shrine is set up, with a fire in the middle and some dead stalkers and heads on sticks scattered around. The thing is that Stalkers don't stay long in that village, much less do anything more than to tell people to avoid it. Which only lets one possible builder open.
After the events of Clear Sky, virtually the entire Clear Sky faction vanishes from the face of the earth. They're never mentioned in Shadow of Chernobyl, and are given an oblique reference in Call of Pripyat. Only two Stalkers you encounter are confirmed to be former members: Nimble, who goes from exhausted rookie Stalker to rookie Stalker in need of rescue to masterarms dealer; and Novikov, who disappears after Clear Sky and reappears working as a technician for the Ecologist faction. Doesn't seem like too big a deal, until you realize that the Monolith faction had a surge in manpower right after the events of Clear Sky.
The stashes. When you first start playing the game and find PD As pointing you to loot containers on the bodies of people you just filled with lead, it seems like a very gamey mechanism to get you to trek around and provide you with progressively better gear. After all, why wouldn't that guy have all that handy stuff on him ? Then as the game goes on, you start getting overloaded with ammo that you're not using right now but might need later, guns and armor that are too nice to just sell (esp. in the first game where you can't repair them), med supplies that you'd be happy to have back after a heavy fight empties your stocks... and that's when you start stashing stuff all over the place like a crazed squirrel yourself, just in case. Congratulations, you're like a real stalker now!
The lack of the Brain Scorcher in Clear Sky. In SoC, you deactivate it and only then does the northward exodus begin as hundreds of Stalkers rush towards Pripyat and the CNPP. In Clear Sky, you just head north without even a mention of any psychic barriers in the way. Why? Because they hadn't been put up yet. The ease with which you and Strelok and an entire flipping faction of Stalkers penetrated the center of the Zone prompted C-Consciousness to put up the Brain Scorcher.