When the array contains only duplicates of a relatively small number of items, a constant-time perfect hash function can greatly speed up finding where to put an item1, turning the sort from Θ(n2) time to Θ(n + k) time, where k is the total number of hashes. The array ends up sorted in the order of the hashes, so choosing a hash function that gives you the right ordering is important.
Before the sort, create a histogram, sorted by hash, counting the number of occurrences of each hash in the array. Then create a table with the cumulative sum of each entry in the histogram. The cumulative sum table will then contain the position in the array of each element. The proper place of elements can then be found by a constant-time hashing and cumulative sum table lookup rather than a linear search.