"Not the least of which" usually follows a plural noun phrase that implies a set of things or qualities, and draws attention to a significant member of that set, e.g.
1. Tom has many engaging qualities, not the least of which is his considerable good humour.
Thus here, the underlined part is the set, and the emboldened part is the significant member of that set.
In your example, which is extremely elliptic, the set is only implicit:
2. Tom is a bad guy, [with many bad qualities], not the least of which [is the fact that] he is always criticizing others.
http://forum.wordreference.com/showthread.php?t=1442830
