Emerald for me. For a couple years (or at least it felt like that) it was my first and only game, so I would endlessly replay it and start over. I remember I could get to Hall of Fame in 16hrs flat consistently. LeafGreen got a lot of play too but I got that later and used to migrate my team to DP which took weeks.
Once I actually had one or two more to play, its honestly hard to say. I don't think I'll have put more hours into a specific save than my current Sword one (406 exactly at last save), but that's my first save on that game. Platinum and HeartGold are my two favourites from Gen IV but I started with Diamond and played that quite a few times before it got damaged. Black must have had at least 6 playthroughs now too.
In terms of time spent - excluding the insane amount of breeding I've done in the Gen 8 games - it'll be either Emerald, Diamond, LeafGreen, or HeartGold I'd imagine - my 2011 Platinum save still existed in 2021 and I did at least 3 playthroughs of HG in that time. Number of saves, Emerald is ahead by an astronomical unit.