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A shader is a (usually not long) parameter list or even program that describes how a surface in a 3D environment behaves. The term "shader" is not perfectly chosen because it insinuates that shaders are only about visual properties or even only about the brightness or color shading of a surface.
Besides describing optical properties to the render software and the graphics card, a shader can also describe game relevant behaviour of surfaces. It can describe a surface as solid or non solid, so you can either walk on or against it or you'd just fall or walk through it. A shader can describe a body as being made of a liquid that you can swim in by giving its surfaces the property "water". In this way, a body can also be described to be lava or poisonous slime.
A surface can be described to sound like metal when walked on. Or it can be made a nobuild-surface so that you cannot make buildings there.
In the Tremulous world, when people talk about shaders, they most probably are talking in the context of mapping. Map makers can create shaders for their maps. They'd maybe create a skybox shader so that they'd not have to use one of the few available skyboxes of the default maps. Or they'd create a new glass texture. Or even an invisible texture with the properties that you cannot walk on it and that shots do not leave marks on it and also not explode when hitting it.
A map's shaders are stored inside the map's .pk3 file in the standard folder "scripts" in the file "nameofmap.shader".
Comprehensive shader manual: www.heppler.com/shader