Start with a frequency count of the number of occurrences of each number between 1 and 100, as Paul suggests. This produces an array freq[] of length 100.
Next, instead of looping over triples A,B,C from that array and testing the condition A^B^C=0,
loop over pairs A,B with A < B. For each A,B, calculate C=A^B (so that now A^B^C=0), and verify that A < B < C < 100. (Any triple will occur in some order, so this doesn't miss triples. But see below). The running total will look like:
Sum+=freq[A]*freq[B]*freq[C]
The work is O(n) for the frequency count, plus about 5000 for the loop over A < B.
Since every triple of three different numbers A,B,C must occur in some order, this finds each such triple exactly once. Next you'll have to look for triples in which two numbers are equal. But if two numbers are equal and the xor of three of them is 0, the third number must be zero. So this amounts to a secondary linear search for B over the frequency count array, counting occurrences of (A=0, B=C < 100). (Be very careful with this case, and especially careful with the case B=0. The count is not just freq[B] ** 2 or freq[0] ** 3. There is a little combinatorics problem hiding there.)
Hope this helps!