They might have a name, I don't know. For the next few lines let us call each a Partial Permutation graph $PP(n,k)$ (assume $k<n$). They may not get as much respect because they are not distance transitive (which the Hamming, Johnson and Knesser Graphs are) or even distance regular (but see below for the special case $k=n$). The Symmetric Group on the underlying set acts on all 4 kinds of graphs and allows one to map any vertex to any other. Consider $n>4$ and $k=2$. In all 4 cases the maximum distance is 2. In $J(n,2)$ any two non-adjacent vertices such as $\lbrace a,b \rbrace$ & $\lbrace c,d \rbrace$ have 4 mutual neighbors. In $H(n,2)$, $[a,b]$ & $[c,d]$ have two mutual neighbors ($[a,d]$ and $[c,b]$) as do $[a,a]$ & $[c,d]$ or $[a,a]$ & $ [c,c]$ and more importantly $[a,b]$ & $[c,a]$ as well as $[a,b]$ & $[b,a]$. I'll leave Knesser graphs for the reader to consider. In $PP(n,2)$ $[a,b]$ & $[c,d]$ still have two mutual neighbors but $[a,b]$ & $[c,a]$ only have one while $[a,b]$ & $[b,a]$ have none. So there are three ways to be at distance $2$. It is a 5-class association scheme of diameter 2 however. For $k=3$ or $k=4$ there begin to be a great number of associate classes. If I calculate correctly, for $n>2k$ $PP(n,k)$ has diameter $k$ but $\binom{k+1}{2}-1$ associate classes (or orbits on pairs of vertices under the action of the automorphism group if you prefer)
In the special case that $k=n$ one would have a graph with $n!$ vertices each of degree $\binom n2$ (one would have to let adjacency be differing in only two positions). Since that is a Cayley graph for $S_n$, it is distance transitive. In the more restricted case that adjacency is that two permutations differ only by the swap of two adjacent positions it is the skeleton of the permutohedron.
later I certainly looked at those graphs at some point. At the time I did not realize that they (seem) to always have all eigenvalues integral (based on a criminally small number of test cases). I wonder if there is an easy way to see that happens (if it does..)