Multiple Effects in a Shader

My question does have a slight basis in GLSL, since that happens to be the shading language I know.

Its my opinion that shaders & the programmable graphics pipeline are a huge step up from the fixed function pipeline. Shaders are excellent at applying effects and making 3D graphics look far more realistic. However, not every effect is meant to be applied to every scenario. For instance, I wouldn't want my flag waving effect used acr开发者_如何学JAVAoss an entire scene. If that scene contains one flag, I want that flag to wave back and forth and thats about it. I'd want a water effect applied only to water. You get the idea.

My question is what is the best way to implement this toggling of effects. The only way I can think of is to have a series of uniform variables and toggle/untoggle them before and after drawing something.

For instance, (pseudocode)

toggle flag effect uniform
draw flag
untoggle flag effect uniform

Inside the shader code, it would check the value of these uniforms and act accordingly.

EDIT: I understand one can have multiple shader programs, and switch on their use as needed, but would this actually be faster than the above method or come with a serious performance overhead from moving all that data around in the GPU? It would seem to be that possibly doing this multiple times per frame would be extremely costly