There should be no pitfalls unless your graphics driver accidentally turns it on for applications that somehow works our GPU so hard it dips below your monitor's refresh rate.
Turning on vSync from your graphics driver control panel (either nVIDIA Control panel or AMD Catalyst, I only talk about these 2) will only force it on on OpenGL dependent applications, so it won't help with the majority of modern games (which usually just use Direct3D anyway). Both nVIDIA and AMD do not allow forcing vSync on Direct3D applications, they state that you need to enable vSync from the respective games' menu.
Applications like Adobe Photoshop IIRC uses OpenGL for its GPU acceleration, but I do not know whether vSync will hamper their ability. Considering that even low-end GPU is usually capable of rendering 2D surfaces at awesome framerate (and it will disable higher level of GPU acceleration anyway), I do not think vSync will be a problem there.
However, like I said the majority of modern games use Direct3D instead of OpenGL, so forcing vSync on globally is not a good idea anyway.