R help - Apr 2011 - Help with multi-response multiple factor model with varying number of factors

This is both a statistics and R question.  I will give more detail if necessary.

What packages of functions would help me to create a mutli-response
model with multiple factors, where the number of levels for each
factor is different?  I have a couple hundred simulation experiments,
and each experiment has four defining factors and 4 continuous and
possibly correlated response variables.  I am not sure if this is
enough information and I will gladly provide more.  I am not sure if I
need to do a manova or go to response surface methodologies, or
something else, and I don't know how to perform the methodologies in
R.  I tried using the manova function in R, but I am having trouble
with specifying the model and finding documentation about how to
interpret multiple response results.  I looked into doing a response
surface model, but I cannot determine if R can handle multiple
responses; the documentation I read says it cannot, but that was
written in 2009.  Any help would be greatly appreciated.

My apologies if this question is too general or is posted to the
incorrect forum.  All guidance is accepted!

Thank your