First, I would suggest not using waterproof mascara or if you do try one that is botanically based or mineral based - such as Bare Escentuals, Arbonne or Origins. These are not so harsh on your lashes and you will probably not have as many lashes fall out.
As for eye makeup remover, I use either Arbonne's makeup remover or Sweet Almond Oil (you can pick it up at your local health food store, Whole Foods or Wild Oats). Supposedly this is what Jackie O used to remove her makeup at night. Another tip is to keep all natural, alcohol free baby wipes on hand. These can be great to use in a pinch or when traveling. They are also great for getting makeup off your clothes!
When you use eye makeup remover, use a cotton pad and do not rub your eyes - this will irritate your eyes and can also cause lashes to fall out. Be gentle!
Good luck!!
p.s. I am NOT affiliated with any particular makeup or skin care line at this time.