This is a list of some of the large software systems that I know. I do not include all of the UNIX utilities that I use everyday, this is larger applications that involve extensive customization and/or configuration.
The list is in descending order of current familiarity. For a few of these my familiarity was only as a power user, but for most it went further, as an administrator or programmer. This page only lists applications, there is a separate page that lists the operating systems that I know.
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And finally, a random note:
There are 10 kinds of people. Those who know binary and those who don't.