A typical application of Benders decomposition to integer programming starts with a problem of the form\[ \begin{array}{lrclcc} \textrm{minimize} & c_{1}'x & + & c_{2}'y\\ \textrm{subject to} & Ax & & & \ge & a\\ & & & By & \ge & b\\ & Dx & + & Ey & \ge & d\\ & x & \in & \mathbb{Z}^{m}_+\\ & y & \in & \mathbb{R}^{n}_+ \end{array} \]This decomposes into a master problem\[ \begin{array}{lrclcc} \textrm{minimize} & c_{1}'x & + & z\\ \textrm{subject to} & Ax & & & \ge & a\\ & h'x & & & \ge & h_0 & \forall (h,h_0)\in \mathcal{F}\\ & h'x & + & z & \ge & h_0 & \forall (h, h_0)\in \mathcal{O}\\ & x & \in & \mathbb{Z}^{m}_+ \\ & z & \ge & 0 \end{array} \]and a subproblem\[ \begin{array}{lrclcc} \textrm{minimize} & c_{2}'y\\ \textrm{subject to} & By & \ge & b\\ & Ey & \ge & d - Dx\\ & y & \in & \mathbb{R}^{n}_+ \end{array} \]where $\mathcal{F}$ and $\mathcal{O}$ are sets of coefficient vectors for "feasibility" cuts (pushing $x$ in directions that make the solution $(x,y)$ feasible) and "optimality" cuts (pushing $z$ upward so as not to underestimate $c_2'y$) respectively. The subproblem is a linear program, and its dual solution supplies the coefficient vectors $(h,h_0)$ for both types of master cuts.
So what happens if $y$ is integer-valued ($y\in\mathbb{Z}^n_+$) rather than continuous ($y\in\mathbb{R}^n_+$)? I don't have a definitive answer, but there are a few things that can be tried. The following suggestions should also work equally well (or poorly) when $y$ is a mix of integer and continuous variables.
Proceed as usual
The subproblem is now an integer program, but you can always relax it to a linear program and obtain the dual solution to the relaxation. If the current master solution $x = \hat{x}$, $z = \hat{z}$ makes the linear relaxation of the subproblem infeasible, you can be sure it also makes the actual subproblem infeasible, and thus you will get a legitimate feasibility cut. If the subproblem is feasible, the dual to the relaxation will produce a cut that forces $z$ to be at least as great as the objective value of the relaxation, which is a legitimate lower bound for the actual subproblem objective value.
The news here is not all good, though. It is possible that $\hat{x}$ makes the subproblem integer-infeasible but with a feasible relaxation, in which case you will not get the feasibility cut you need. If the subproblem is feasible (let's say with optimal solution $\hat{y}$) but $\hat{z}$ underestimates its objective value $c_2'\hat{y}$, you want an optimality cut that forces $z\ge c_2'\hat{y}$ when $x=\hat{x}$; but the cut you get forces $z\ge w$ where $w$ is a lower bound for $c_2'\hat{y}$, and so there is the possibility that $c_2'\hat{y} > \hat{z} \ge w$ and the optimality cut accomplishes nothing.
"No good" constraints for infeasibility
Suppose that $x$ consists exclusively of binary variables. (General integer variables can always be converted to binary variables, although it's not clear that the conversion is in general desirable.) We can exclude a particular solution $x=\hat{x}$ with a "no good" constraint that forces at least one of the variables to change value:\[\sum_{i : \hat{x}_i=0} x_i + \sum_{i : \hat{x}_i = 1} (1-x_i)\ge 1.\]This gives us another option for feasibility cuts. Solve the subproblem as an IP (without relaxation); if the subproblem is infeasible, add a "no good" cut to the master problem. Note that "no good" cuts are generally not as deep as regular Benders feasibility cuts -- the latter may cut off multiple integer solutions to the master problem, whereas a "no good" cut only cuts off a single solution.
If a "no good" cut eliminates just one solution, is it worth the bother? After all, the node that produced $x=\hat{x}$ will be pruned once we realize the subproblem is infeasible. The answer depends on a combination of factors (and essentially reduces to "try it and see"). First, if $x=\hat{x}$ was produced by a heuristic, rather than as the integer-feasible solution to the node LP problem, then you likely cannot prune the current node (and, in fact, the node you would want to prune may be elsewhere in the tree). Adding the "no good" cut may prevent your ever visiting that node, and at minimum will result in the node being pruned as soon as you visit it, without having to solve the subproblem there. Second, if your master problem suffers from symmetry, the same solution $x=\hat{x}$ may lurk in more than one part of the search tree. The "no good" cut prevents your tripping over it multiple times.
It may be possible to strengthen the cut a bit. Suppose that $\hat{x}$ renders the subproblem infeasible (as an IP). There are various ways to identify a subset of the subproblem (excluding the objective function) that causes infeasibility. CPLEX can do this with its conflict refiner; other solvers may have similar functionality. Let $N$ be the set of indices of the $x$ variables and $N_0$ the set of indices of all $x$ variables that appear in the right hand side of at least one subproblem constraint identified as part of the conflict. If we are lucky, $N_0$ is a proper subset of $N$. We can form a "no good" cut for the master problem using just the variables $x_i, i\in N_0$, rather than all the $x$ variables, and obtain a somewhat deeper cut (one that potentially cuts off multiple master problem solutions). The caveat here is that running something like the CPLEX conflict refiner, after determining that the subproblem is infeasible, may eat up a fair bit of CPU time for questionable reward.
"No good" constraints for optimality
It may be possible to exploit the technique I just described to create ersatz optimality constraints as well. Suppose that the current incumbent solution is $(\tilde{x}, \tilde{y})$, and that some node gives an integer-feasible solution $(\hat{x},\hat{z})$ for the master problem. It must be the case that\[c_1'\hat{x}+\hat{z}<c_1'\tilde{x}+c_2'\tilde{y},\]else the master problem node would be pruned based on bound. Now suppose we pass $\hat{x}$ to the IP subproblem and obtain an optimal solution $y=\hat{y}$. If $c_1'\hat{x}+c_2'\hat{y}<c_1'\tilde{x}+c_2'\tilde{y}$, we have a new incumbent solution. If not, then $x=\hat{x}$ cannot lead to an improved solution, and we can add a "no good" cut to eliminate it (again recognizing that this is a weak constraint).
More?
That pretty much exhausts my quiver. If any readers have other ideas for generating Benders cuts from integer subproblems, I invite you to post them in comments.