Shader inputs in a general purpose engine

Yes, they do allow custom uniforms, but they will also fill out a few standard ones. For example, I'm using Horde3D for a project, and one of the shaders contains the following:

[[VS_GENERAL]]

#include "shaders/shaderSettings.shader"

#include "shaders/utilityLib/vertCommon.glsl"

#ifdef _F01_Skinning
    #include "shaders/utilityLib/vertSkinning.glsl"
#endif

uniform mat4        viewProjMat;
uniform vec3        viewerPos;
attribute vec3      vertPos;
attribute vec2      texCoords0;
attribute vec3      normal;

#ifdef _F02_NormalMapping
    attribute vec4  tangent;
#endif

varying vec4        pos, vsPos;
varying vec2        texCoords;

#ifdef _F02_NormalMapping
    varying mat3    tsbMat;
#else
    varying vec3    tsbNormal;
#endif

varying vec4        projCoords;

// texture matrix
uniform vec4        textureMatrixRow0;
uniform vec4        textureMatrixRow1;
uniform vec4        textureMatrixRow2;
uniform vec4        textureMatrixRow3;

And the material:

<Material>
    <Shader source="shaders/water.shader" />

    <ShaderFlag name="_F01_Skinning" />
    <ShaderFlag name="_F02_NormalMapping" />
    <ShaderFlag name="_F02_Character" />

    <Sampler name="albedoMap" map="/textures/dolphin/dolphin_diffuse_V02.dds" />
    <Sampler name="causticMap" map="/textures/caustics/001.dds" />
    <Sampler name="normalMap" map="/textures/dolphin/dolphin_normal_V02.dds" />

    <Uniform name="textureMatrixRow0" a="0.0" b="0.0" c="0.0" d="0.0" />
    <Uniform name="textureMatrixRow1" a="0.0" b="0.0" c="0.0" d="0.0" />
    <Uniform name="textureMatrixRow2" a="0.0" b="0.0" c="0.0" d="0.0" />
    <Uniform name="textureMatrixRow3" a="0.0" b="0.0" c="0.0" d="0.0" />
    <Uniform name="fogColor" a="0.0" b="0.0" c="0.0" d="0.0" />
    <Uniform name="texScale" a="1.0" b="0.0" c="0.0" d="0.0" />
</Material>

Here, the viewProjMat and viewerPos uniforms are filled by the engine, while the others are defined by the user. It seems like a pretty good solution to me.

Note that you can check which GLSL uniform variables are actually used in a shader program:

// uniforms

GLint max_name_length;
GLint active_count;
GLchar* name;
GLsizei length = 100;
GLenum type;
GLint size;

glGetProgramiv(m_Program, GL_ACTIVE_UNIFORMS, &active_count);
glGetProgramiv(m_Program, GL_ACTIVE_UNIFORM_MAX_LENGTH, &max_name_length);

name = new GLchar[max_name_length];
for (GLint u = 0; u < active_count; u++)
{
    glGetActiveUniform(m_Program, u, max_name_length, &length, &size, &type, name);
    GLint handle = glGetUniformLocation(m_Program, name);

    LOG_INFO("Uniform - %s (%i)", name, handle);

    if (!strncmp(name, "gl_", 3))
    {
        LOG_TRACE("Using deprecated GLSL: %s", name);
    }
    else
    {
        // do something with standard uniforms
    }
}
delete [] name;

EDIT:

As a user, you see the following:

// set the fog color uniform
h3dSetResParamF(res, H3DMatRes::UniformElem, 4, H3DMatRes::UnifValueF4, 0, m_FogColor.x);
h3dSetResParamF(res, H3DMatRes::UniformElem, 4, H3DMatRes::UnifValueF4, 1, m_FogColor.y);
h3dSetResParamF(res, H3DMatRes::UniformElem, 4, H3DMatRes::UnifValueF4, 2, m_FogColor.z);

Can't say I agree with the C-style interface, but it works.