What is a clip brush?
A special brush in the Quake engine. Any brush covered on all faces by the CLIP texture is considered by the BSP compile tools to be a clip brush. A clip brush is unique in that it appears in the clipping hull but not the visual hull. Practically speaking, that means that the player cannot pass through it, but nor can they see it.
What purpose does the clip brush serve?
At least two:
Example 1: Say you are building a streets-based level, but you want to block off a certain road. You could place road blocks or similar across it - indeed, you should; but chances are, some player will find a way to crawl through them, or at least get themselves stuck trying, and either way it reduces realism in the level.
The solution is to build the road block, but then build a large clip brush right over the whole road, and right up to the sky. The player can no longer sneak round the road block, but everything looks usual. As an added bonus, they can still fire through the clip brush, just as in real life.
Example 2: VIS can take a long time to compile very detailed architecture. A lot of time is wasted dividing up the small details of the solids into convex polyhedra. Alternatively, you can place one large clip brush over the whole lot, saving the compiler the trouble. The player will notice no difference, because they can't get into such tiny gaps anyway.
On the other hand, you can make very detailed clip brushes, which may compile slower, but the end map will have no difference in frame rate. As the clip brush is not drawn, it consumes no processor cycles.
Why not just use 100% transparent glass?
The player can't fire through the glass, so it will appear that there is some invisible force field blocking them and their bullets. Maybe this is the effect you want; in which case, by all means use glass.
Also, with the older compile tools at least, the graphics card is still forced to "draw" the glass, even though it has no actual visual effect. Hence you may lower the frame rate somewhat.
How do they work?
This is somewhat technical and not important to the majority of mappers, but you may be interested in the theory behind it
The whole clip brush handling is invisible to the Quake engine, it is actually all done in the compilers; QBSP in fact. In short, the Quake engine has four different hulls, which you could think of as interpretations of the map. Three of the hulls are clipping hulls, ie they are concerned with blocking entities, or letting them pass. For example, a wall is in the clipping hull, because it blocks the player's passage. The other hull is a visual hull, concerned with what players can actually see.
When QBSP or it's equivilant encounters a brush covered in the CLIP texture, it places it into the clipping hull that controls entity movement; so entities are blocked by the clip brush just like any wall. However, it does not place them into the clipping hull that controls bullet movement, so bullets pass through just as if nothing were there. It also omits them from the visual hull; so the player sees nothing. The engine is not told to draw the clip brush, so it does not.
It should now be obvious why you can make clipping brushes as complex as you like without any performance hit at run time.