I'd use IPC::Run... It's consistent, relatively easy to use, and very flexible.

I especially like using callbacks for output collection and input generation.

As for IPC::Open2 and IPC::Open3 and all those - i don't like them because they're inconsistent with each other, and have no way to do easy things like "the input is this string", or "slurp the output into this var" and so on.

Furthermore, IPC::Run has nice tools to abstract select loops (see pump), and in that way makes deadlock avoidance easier.