How can I run an external program from C and parse its output?

As others have pointed out, popen() is the most standard way. And since no answer provided an example using this method, here it goes:

#include <stdio.h>

#define BUFSIZE 128

int parse_output(void) {
    char *cmd = "ls -l";    
    
    char buf[BUFSIZE];
    FILE *fp;

    if ((fp = popen(cmd, "r")) == NULL) {
        printf("Error opening pipe!\n");
        return -1;
    }

    while (fgets(buf, BUFSIZE, fp) != NULL) {
        // Do whatever you want here...
        printf("OUTPUT: %s", buf);
    }

    if (pclose(fp)) {
        printf("Command not found or exited with error status\n");
        return -1;
    }

    return 0;
}

Sample output:

OUTPUT: total 16
OUTPUT: -rwxr-xr-x 1 14077 14077 8832 Oct 19 04:32 a.out
OUTPUT: -rw-r--r-- 1 14077 14077 1549 Oct 19 04:32 main.c

popen is supported on Windows, see here:

http://msdn.microsoft.com/en-us/library/96ayss4b.aspx

If you want it to be cross-platform, popen is the way to go.

For simple problems in Unix-ish environments try popen().

From the man page:

The popen() function opens a process by creating a pipe, forking and invoking the shell.

If you use the read mode this is exactly what you asked for. I don't know if it is implemented in Windows.

For more complicated problems you want to look up inter-process communication.