Animating properties is never free. GPU don't matter none. Some animations are more costly than others, though. Keep the transitions that trigger
layout to a minimum.
Also whatever you do, make sure your site will perform at a steady 60fps. Everything else will result in stutters. Save your frames!
So basically, if you want to make sure you do nothing wrong, only ever use transform and opacity.
If you want to dive deeper into this topic and find out what costs what, you can find an overview here.
P.S.: If you want do build a material design website, why don't you #usetheplatform, namely Polymer ?