Known packages for working with network-like data
(need to create better category system / tagging so they are not exclusive)
Rather than linking directly to the software's page (which can hopefully be found with a web search), some of these point to a page on the wiki cataloging links to the software's main site, supported formats, OS, authors, etc. to try to make it easier to compare some programs. For example, see Pajek. Of course, there are many piece of software beyond those listed below.
Modeling / Stats
Libraries / Code Repositories
the Krugle source code search engine is very useful (but still in beta)
Links to other lists of software