%s is a C format specifier for a string.

msg = g_strdup_printf (_("<b><big>Enter your password to run "
                         "the application '%s' as user %s"
                         "</big></b>"),
                         command, context->user);

means "where you see the first %s, replace it with the contents of command as a string, and where you see the second %s, replace it with the contents of context->user as a string.

%s most likely means a string. Sort of like a placeholder or variable.

In some languages you can write something like:

string name = "Joe";
printf("Hi %s", name);

Which would print out: "Hi Joe".

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"/s" is suppose to imply sarcasm.