Let me know if you can break it, I actually think I got it right (famous last words)

# each filename is wrapped in quotes
# so we only need to escape characters which have
# special meaning to the shell - when it interpolates
# in double-quotes. there are only 4 such characters,
# namely " ` $ and \
# interestingly, newline is NOT one of these... 

sub quote_for_shell {
   my ($x) = @_;
   $x =~ s/([\"\`\$\\])/\\$1/g;
   return "\"" . $x . "\"";
}

@command_line = (
   quote_for_shell( $prog1 ),
   quote_for_shell( $file1 ),
   "|",
   quote_for_shell( $prog2 ),
   "-x -y",
   "|",
   quote_for_shell( $prog3 ),
   ">",
   quote_for_shell( $file3 )
)

system join " ", @command_line;
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I tested this successfully on a randomly generated directory tree full of randomly-generated filenames made up of chr(rand(128)) except "/" and "\0". Actually, $prog1, $file1, etc can have "/" in them because they might be pathnames.