[ux, ~, xidx] = unique(data(1,:));
[uy, ~, yidx] = unique(data(2,:));
%count the number of points at each unique x/y combination
counts = accumarray([xidx(:), yidx(:)], 1);
%average the z that fall into each unique x/y combination
avgs = accumarray([xidx(:), yidx(:)], data(3,:).');
%create a list of the z that fall into each unique x/y combination
zs = accumarray([xidx(:), yidx(:)], data(3,:).', [], @(V) {V}, {});
But perhaps what you want is instead a 2D histogram:
or if you have an older version: