My next suggestion (I don't have time to work out or test an example
at the moment):

library(abind)
tmparr <- abind(m1,m2,m3,...,along=3)
  OR
tmparr <- do.call(c(matlist,list(along=3)))
apply(tmparr,c(1,2),mean,na.rm=TRUE)

  or something along those lines.

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