Hi.  There's a tool called Firewalk which may be worth checking out, and there's a tool which looks like it's designed to audit Cisco firewalls/routers called Router Audit Tool; see http://www.cisecurity.org/bench_cisco.html

The only reason that Angry IP scanner can work is that it is looking for what services are listening on the target host/s.
A lot of viruses/malware don't listen on the target host/s; and I would guess that most worms are not following usual protocols, so scanning infected hosts with listening ports is not going to give you reliable results.
There's at least one tool I know of which does what you want, but it only does it for one worm: eEye/Retina's Sapphire SQL Worm Scanner.  I think they did one for Nimda also.