Some I don’t see mentioned yet:

• Simon Tatham’s Portable Puzzle Collection ported to pretty much everything.
• Nethack (and its variants), Dungeon Crawl Stone Soup and Brogue are great roguelikes.
• For boardgame fans the original Keldon AI for Race for the Galaxy is open source and works very well on Linux.
• Fish Fillets NG is one I have fond memories of from many years ago.
• The Ur-Quan Masters is Star Control 2, another classic.