Similar to last week's two posts about simple thing that are easy to forget, we also have the fact that not all properties of HTML elements and not all CSS style properties can be animated with CSS animations and transitions (including WinJS.UI.executeTransition and similar helpers). For example, someone asked a question a while ago about some code that was attempting to animate an element's scrollLeft property, but it wasn't working. This is simply because scrollLeft isn't an animatable property! In that case, the proper answer is to animate the desired motion using the transform property.
I have to say that I don't know where a definitive list exists of what properties can or cannot be animated, but let me frame the question differently. When you use CSS animations or transitions on the transform and/or opacity properties, those animations will run "independently" in the GPU. Animating anything else–if it can be animated–runs "dependently" which means in the CPU and on the UI thread, which will typically perform poorly on less powerful devices. Similarly, you can always animate any property you want using requestAnimationFrame, but those always run on the UI thread as well.
The best practice, in short, is to always think how you can achieve the effect you want through transform and opacity. If you can't, and must do a dependent animation, try it with CSS animations/transitions, and if that doesn't work, then roll your own with requestAnimationFrame.