Robin Girad commented in regards to this question:
the question in addition to the answers make me think this should be stackexchange... there should be a discussion on meta about questions with "how to speed up"
I (obviously) disagree that stack exchange is the appropriate place for this question. Per the consensus here and here it seems that programing questions with any statistical content should be welcome on this site. Optimization of statistical calculations require consideration of the calculations being performed and assurances that their integrity is not going to be compromised. Further, the sort of functions likely to be discussed will be familiar to the audience here but not on StackOverflow. For example, in the reference question mbq quickly saw that using diag() was throwing away a lot of effort because he is familiar with R and the notion of taking the diagonal from a matrix. Would I really have gotten an answer with that insight as rapidly elsewhere?
Do we need to have further discussion on this issue?