If you want alternative lighting calculations or shading effects (beyond color shift) you can do it in a few ways.
The first way would be to create a separate object that uses the vertices you want to be rendered, and either render the original object without these vertices, or simply overdraw the same vertices with the new effect. The overdraw is likely to be more efficient than the time it would take to sort out vertex buffer and index buffer organization. You may also need to remove z-testing for the effects pass.
The second way would be to modulate specific vertices color, and render them a very specific color that is not present in your game in any other fashion (such as a vibrant pink). After that, you could perform glow effects or whichever as a post processing step, that only acts on anything rendered using this particular color. The color of course is only being used as an obvious identifier. This method would likely be best if you are rendering many different objects in this way. Edit, also for this particular effect, you will have to avoid texture sampling in this situation one way or another, otherwise it will be blended with the modulated vertex color, producing inconsistent color variations.
The last way I could think would be to actually implement branching code in whichever shader is applied to objects that could have this effect. I highly advise against this, as branching code is problematic and generally much slower on GPU's, and you REALLY dont want a default shader to have branching code in it. You could perform a shader swap though whenever this effect is enabled, and test the performance characteristics of it. This would also require additional data overhead, as each vertex would need a flag indicating whether it is currently part of the desired effect, or rendered normally. This is the worst of the three by far, but it is an option.
