Web browsers: elinks, based on links, which I'm pretty sure was a play on words on lynx, which is a play on words on "links" on a web page.
Then there's email. There's mahogany and balsa and mulberry, which are in-jokes referring to pine, which was a joke referring to elm, which stood for ELectronic Mail. Pine has been forked to alpine, in an entirely different play on words.