How can I best bake cookies from cold dough? I like to make chocolate chip cookies, and the first batch always turns out great. However I don't use all the dough at once, so I refrigerate the leftovers. When I use this cold dough to make another batch of cookies, they are usually a little overdone on the outside while still a bit underdone on the inside. 

I've tried setting the dough out on the counter for a while to let it warm up to room temperature, but even sitting out for over an hour, it hasn't noticeably changed temperature. I've also tried rolling the balls of dough in my hands for a bit to warm them before placing them on the pan, but that seems to make the issue worse (probably because the outside melts before the inside thaws). This leads me to think any other solution (microwaving the dough, putting the pan in a slightly warm oven, etc) will make things worse rather than better.

Is there some easy solution I'm not thinking of besides making dough in smaller batches (which is tough because you can't go down to less than one egg)? Do I need to store the dough in a different way or prep it somehow before baking?

I generally use the recipe on the back of the bag of Tollhouse chocolate chips, which uses butter, sugar, brown sugar, eggs, flour, etc. I use real butter, not margarine or shortening.
Bake it all and freeze some cookies.

Cookies freeze great.  And you can let them sit out overnight to thaw without worries.