We show that the moduli space of the $(2,0)$ and little-string theories
compactified on $T^3$ with R-symmetry twists is equal to the moduli space of
U(1) instantons on a non-commutative $T^4$. The moduli space of $U(q)$
instantons on a non-commutative $T^4$ is obtained from little-string theories
of NS5-branes at $A_{q-1}$ singularities with twists. A large class of gauge
theories with ${\cal N}=4$ SUSY in 2+1D and ${\cal N}=2$ SUSY in 3+1D are
limiting cases of these theories. Hence, the moduli spaces of these gauge
theories can be read off from the moduli spaces of instantons on
non-commutative tori. We study the phase transitions in these theories and the
action of T-duality. On the purely mathematical side, we give a prediction for
the moduli space of 2 U(1) instantons on a non-commutative $T^4$.