jnget is a multi-platform command line tool to retrieve binaries from Usenet. It allows multi-thread downloading and partial or full headers updating and caching and has NZB support.
IntiMap is a convenience tool to run the MS-DOS command-line tool MapPop for selective genotyping. It adds facilities to prepare genotyping data files, manage genotype sets and visualize mapping results (genetic marker maps).
Synclair is a tool for diff'ing and synchronizing directories. It also includes a utility to find duplicate files (by name, or md5 hash). It is a command line tool, written in Java.