Emphasizing size:
* Eyes like saucers
* Eyes like two big, round pools
* Eyes as large as dinner plates
* Eyes that could stare a hole through you
* Eyes that seem to bulge out of their sockets
Emphasizing other qualities:
* Eyes like bright, shiny marbles
* Eyes like wide-open windows to the soul
* Eyes that sparkle like stars
* Eyes that seem to hold a universe within them
* Eyes as deep and mysterious as the ocean
The best simile will depend on the specific context and the effect you're trying to achieve.