Fisher's exact test is available for r x c tables, too (with r>2 and/or c>2). Only the odds ratio statistic cannot be calculated in non-2x2-tables.
Mehta, C. R. and Patel, N. R. (1986) Algorithm 643. FEXACT: A Fortran subroutine for Fisher's exact test on unordered r*c contingency tables. ACM Transactions on Mathematical Software, 12, 154–161.
Clarkson, D. B., Fan, Y. and Joe, H. (1993) A Remark on Algorithm 643: FEXACT: An Algorithm for Performing Fisher's Exact Test in r x c Contingency Tables. ACM Transactions on Mathematical Software, 19, 484–488.
Patefield, W. M. (1981) Algorithm AS159. An efficient method of generating r x c tables with given row and column totals. Applied Statistics 30, 91–97.
there are dozens of alternatives whose suitability and efficacy depend on the features of your data. Are they categorical, ordinal or interval variables? Are they continuous or discrete? Do they shows (un)known distributive profiles to be compared?
For example, if you have continuous, one-dimensional probability distributions KS test can be used to compare a sample with a reference probability distribution (one-sample KS test), or to compare two samples (two-sample KS test) - http://en.wikipedia.org/wiki/Kolmogorov–Smirnov_test
Similarly, Anderson-Darling Tests may help you without any hypothesis about continuity of the underlying distribution - http://www.jstor.org/stable/2288805?seq=1#page_scan_tab_contents
Conversely, if you have a-priori knowledge about the distribution form, other parametric test might suit better your case. For categorical data, again, it's another story.
If you could characterize better your problem I'll be happy to help you.