I lost my first Morrowind save file. 200 hours invested, and a character that I'd finally gotten to a point where he was powerful enough I could just breeze through the tedium the combat is in that game to keep exploring the world.
Also, not really "loss", but a stupid delete that I didn't realize until much later. On one of my first playthroughs of Pokemon Crystal I caught a shiny Pidgey very early on. I'd heard about shiny Pokemon before, but I didn't know just how insanely rare they were (1/8192 chance). I was unhappy with my starter choice (something about Chikorita's back sprite still irks me for no apparent reason to this day), and I re-started the game, assuming that I'd likely just get another shiny in the process. That Pidgey is, to this day, one of only three shiny Pokemon I've ever caught.