Minimize the sum of squared one-step forecast errors. If $\hat{Y}_t$ is the prediction of $Y_t$ given $Y_1,\dots,Y_{t-1}$, then $e_t=Y_t-\hat{Y}_t$ is the one-step forecast error. So minimize $e_2^2+\cdots+e_n^2$.
You can also use maximum likelihood estimation as discussed in my Springer book.
If you're just using simple exponential smoothing, and are happy to assume normal errors with constant variance, then an ARIMA(0,1,1) model is equivalent.
When you use a state space representation (such as in the innovations state space form, or by writing the ARIMA model in state space form), then handling missing values is easy. For example, the R function arima() will handle missing values without complaint.