I wouldn't do this as a one-liner, but of course you can. But rather than loop through your IPs and check each of them against the other file (or vice versa), put the IPs in a hash, then go through the other file looking for IP patterns, check them against the hash, and comment them if they're found.
$ cat ips
111.222.333.444
55.66.77.88
$ cat text
Line 1 nothing to comment
Line 2 111.222.333.444 should be commented
Line 3 11.22.33.44 do not comment
Line 4 55.66.77.88 should be commented
$ perl -pe '@l = `cat ips`;chomp @l; %h = map {$_=>1} @l; s/(\d{1,3}\.
+\d{1,3}\.\d{1,3}\.\d{1,3})/$h{$1}?"#$1":$1/e;' <text
Aaron B.
Available for small or large Perl jobs and *nix system administration; see my home node.