Counter-Strike is a vague term which blanket references all the games in the Counter-Strike line-up: Counter-Strike 1.6, Counter-Strike: Condition Zero, and Counter-Strike Source.
When people refer to Counter-Strike, they most likely mean Counter-Strike 1.6, the most up-to-date version of the original Half-Life mod, but they could be referring to any of them. All of the games also have several popular nicknames or abbreviations amongst their players: CS, 1.6, or Counter-Strike for Counter-Strike 1.6; CSS, CS:S, or Source for Counter-Strike Source; CZ, CS:CZ, or Condition Zero for Counter-Strike: Condition Zero.
If you are refering to the difference between Counter-Strike 1.6 and Counter-Strike: Source the differences are this:
Counter-Strike source being a newly made game has improved graphics, textures, physics and game play. The recoil dynamics and "Feel" of the game is much different from 1.6. In source maps have much more detail and high-res textures than in 1.6. Also, in Source a lot of the exploits of 1.6 were changed such as Crouch Hopping (Tapping your crouch button once, and then hitting it again and holding it would make your character "dip" down into a crouch position making the hit boxes of your character scramble, making a well placed head shot register as a well placed arm shot) Also, the radar has been changed. In 1.6 it was a small green circle on your screen showing dots for your allys and no one else. In Source the Radar is a large box that shows detail of the map, and it will show enemies if they fire a unsuppressed weapon.
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