Many institutions and authors develop repositories and not all are completely open access. Most, if not all of the actively growing repositories use software that allows the author complete control over who sees her/his work. The flexibility allows authors the choice of making their works, as a body or as individual arcticles, available or not and allows them to retain complete control. Also citation counting capability is becoming standard for these comprehensive software packages.
The effects of this control are discussed in a recent article in Citebase.