This depends on what you define as in game. According to Steam, I've spent the most time on NGU Idle at 3306 hours, but a large amount of that was spent with the game running while I was asleep or at work. For Steam games with the most hours, I've spent 840 playing Path of Exile but that doesn't include the 200 or so hours playing the standalone client. This is followed up by 440 hours playing Terraria (which doesn't include console version hours), and Realm of the Mad God which I have 325 hours playing.
If we include MMOs in the mix, I've easily clocked 1500 hours playing both World of Warcraft (between Classic and Retail up to and including Mists of Pandaria) and Guild Wars 2 over the years.
Funny enough, I wouldn't include any of these games in a list of my favorite games other then Terraria, so that's good to keep in mind :)