I think you're forgetting about the Animation API.

Example: making something flash once to get a user's attention

element.animate( {opacity: [1, 0, 1]}, { duration: 500 } );

Use CSS animations everywhere you can, but if you need to be able to hook into an animation (to dynamically change the speed, cancel something, sync animations together, etc...) you should be using the Animation API.

There's never a need for jQuery.