Yes, this statistic doesn't require equal sample size, equal variance, or stuff like that. See e.g. http://www.physics.csbsju.edu/stats/KS-test.html, http://stats.stackexchange.com/questions/47498/mann-whitney-u-test-and-k-s-test-with-unequal-sample-sizes.
The KS method is a very reliable test. Nevertheless, it can be a little hard on data some times. The chi-squared test sets a lower goal and tends to refuse the null hypothesis less often.
I think this book will provide you with many alternatives for performing statistical tests, and with useful explanations:
2006, Kanji, Gopal K., "100 Statistical Tests", Third Edition, Sage Publications.