Commonly, I use the MANOVA statement in the GLM procedure of SAS (general linear models) to perform a multivariate analysis of variance on continuous dependent variables. Also, I use the statement DIST=BIN in the GENMOD procedure of SAS (generalized linear models) to perform logistic regression on binomial dependent variables.
To my knowledge, I cannot perform a MANOVA using binomial dependent variables, but I suppose that some way to do it must exist.