Some of the biggest "mods" don't actually require you to install them into your Call of Pripyat folder. They use the game's engine but function as separate games:

Guide :: S.T.A.L.K.E.R. - Call of Chernobyl: Modding the Zone

: A gameplay and graphics modpack designed for a fresh, consistent experience in the final game of the trilogy.

: Copy the gamedata folder (and sometimes a bin folder) into your main S.T.A.L.K.E.R. Call of Pripyat directory.