Duncan was picked #1 in the 1997 draft, which made NBA Live 98 his first video game appearance.
And with 2015-16 being his last season, that makes his final video game appearances those in NBA 2K16 and NBA Live.
NBA Live 16
With both Kobe and Duncan now out of the NBA, the ranks of players to have appeared in every 2K game (Kevin Garnett, Vince Carter, Paul Pierce, Dirk Nowitzki & Nazr Mohammed?) grows thinner. As for NBA Live, nobody is still around who's played in every game from that series, which debuted in 1994 (though Garnett comes close!).