I've been mulling (yes, mulling) replacements for RKH's suspscan for a while now. Suspscan was an experiment to see if there could be a more generic, less name-based way of finding malware. The resultant monstrosity is resource-intensive, impossible to configurable and rarely used. Researching something else (as usual) I came across this rather good presentation (PDF) about creating ones own AV signatures:
Writing ClamAV Signatures and not long after that I found R-fx Networks'
Linux Malware Detect....