An example to illustrate:
Say I have 3 digits, to be taken from the set $\{1,2,3\}$.
I want to choose from this set of digits, with repetition allowed, to make triplets.
However, no two triplets should be attainable through permutation of the triplet - e.g:
$001$ can be permuted to $010$
$201$ can be permuted to $012$
but $011$ and $001$ are "permutationally independent" (any help on the proper name for this appreciated)
In this case, the set of all possible triplets is $\{000, 001, 011, 111, 002, 022, 222, 012, 112, 122\}$, and there are $10$ possibilities.
How could I have worked out this number without manually enumerating the possibilities? And how could this be done for forming n-tuples from a set of k possible digits?
I have tagged this question with some group theory tags, as am expecting from my own thinking that the answer can probably be quite neatly given in terms of dihedral group actions and orbits, though I may be wrong.
You can use stars and bars (Theorem 2) to count this. For your general "$n$-tuples from a set of $k$ digits" question, it yields $\binom{n+k-1}{n-1}$. In the special case $n=k=3$, this is $\binom{5}{2}=10$, which matches your manual enumeration.