Runtime.getRuntime().exec("C:\meuprograma.exe");

src
 |__ br.foo.files
 |__ br.foo.main

Runtime.getRuntime().exec("files/meuprograma.exe");
Runtime.getRuntime().exec("./files/meuprograma.exe");
Runtime.getRuntime().exec("/files/meuprograma.exe");

File home = new File(System.getProperty("user.dir"));
File file2 = new File(home, "files/meuprograma.exe");
Runtime.getRuntime().exec(file2.getPath());