http://img213.imageshack.us/img213/6300/areaportalin7.jpg areaportal Blocks vis when a door is closed, to function the brush has to be textured with the "skip" shader and ONE face has to be textured with the "areaportal" shader, then the face with the "areaportal" shader has to be exactly in the middle of the door.
This is the most common system shader, this shader is invisible and all faces with this shader wont be drawn by the engine, therefore this shader should be on any face the player cant see.
http://img138.imageshack.us/img138/3453/caulkbk5.jpg caulk_noclip Same as caulk, but this one also makes the brush non-solid i.e. you can walk though it.
http://img138.imageshack.us/img138/3453/caulkbk5.jpg caulk_water Same as the normal caulk, but this one gives the brush water properties i. e. Splash sounds, drowning and stuff like that.
http://img467.imageshack.us/img467/4692/clipdy0.jpg clip This shader is completely invisible ingame and will block players, NPCs and BOTs, but missiles, blasters and grenades will get though. This is useful for making stairs and stuff like that.
http://img213.imageshack.us/img213/8865/cushionxg9.jpg cushion If a player lands on a brush with this shader he will not take any falldown damage. Caution: this will also remove any landing sounds, so use carefully.
http://img467.imageshack.us/img467/2305/hintuf0.jpg hint This shader is used to block vis around corners, it has to be placed so that it is overlapping 8 units with structural brushes in all directions. for further information check this tutorial.
http://img120.imageshack.us/img120/343/insideuj7.jpg inside If you have any weather effects(like rain, snow) in your map, you should place this brush everywhere you don't want the weather effect to appear, like inside buildings. Note: This CANT be used in combination with the "outside" shader.
http://img467.imageshack.us/img467/6498/nodroput5.jpg nodrop This nonsolid shader will prevent players who die when they are inside a brush textured with this shader from dropping their weapons. This is useful in pits-of-death to stop the models in the pit stealing FPS.
http://img213.imageshack.us/img213/8391/noimpactsi7.jpg noimpact No explosions occur when projectiles strike this surface and no marks will be left on it. Sky textures are usually marked with this texture so projectiles will not hit the sky and leave marks.
http://img151.imageshack.us/img151/701/originiz5.jpg origin This shader is used on brushes to specify the center(or just the place the engine is supposed to think the center is) of some entities, like func_statics or func_trains. All rotating things will rotate AROUND the origin brush and moving things will move the origin brush(and because its connected to the rest the rest will move too).
http://img120.imageshack.us/img120/3382/outsidegf1.jpg outside Same as the "inside" shader, but this time it specifies where to play the rain effect, place this shader where you want to have rain. Note: This CANT be used in combination with the "inside" shader.
http://img213.imageshack.us/img213/4503/physicsclipqg9.jpg physics_clip Same as clip, except this one blocks everything except visibility, this is very useful to clip models.
http://img120.imageshack.us/img120/5699/rainsurfup5.jpg rainsurf Surfaces with this texture on them will(should) enable that rain-splatter effect. Although Smoke says it does not work.
http://img467.imageshack.us/img467/3538/shotonlyclipzu4.jpg shotonlyclip Same as clip but only blocks blaster shots. Rockets, and grenades will pass.
http://img295.imageshack.us/img295/4386/slickqa4.jpg slick This shader will make the surface its on slick, that means you will glide and cand change direction.
A player inside this shader will be able to trigger a event. the event is specified in the map editor.
http://img120.imageshack.us/img120/6841/terrainql4.jpg terrain This is one of the most complex shaders, it will allow you making nice terrains with blended textures. To see how this is used, go Help > General > Terrain Manual in GtkRadiant.
If you have inside or outside shaders in your map, try to enclose them into brushes textured with the "weatherzone" shader. This isn't necessary but will improve the FPS.