I suppose it depend on what purpose you are using the cotton balls for--that might help in finding an alternative :)

I used to use cotton balls for doing things like removing my nail polish...but I found that a regular wash cloth works fine for that, and is reusable.

Squares of flannelette?

I use a wash flannel for removing make-up-I have a handy little hook that it hangs on next to the sink.

Etsy has a handful of crocheted alternatives that are good for removing eye makeup.

Better for GrownUps has recently introduced reusable organic cotton velour rounds just for this purpose. Customers at our store seem pleased with them and several have made a point to come back and say that they really like them. You get 30 in a reusable cardboard dispenser box, as well as an organic cotton mesh bag for washing them.

We sell them at our store:
http://www.greenwardshop.com/shop/home/body-care/new/bath/8093-organic-velour-cotton-rounds-box-of-30/

Manufacturers' page:
http://www.betterforgrownups.com/organic_cotton_face_rounds_p/bfgfr00.htm

Scott Walker, Owner
Greenward

Microfibre washcloths, cut small. The fluffier, the better.