If I was a betting man, I'd have put money on Enderal, the vast Skyrim total conversion, winning the public vote for ModDB's mod of the year. That I'd have lost all that money is why I'm not a betting man. Enderal came second behind Stalker: Call of Chernobyl, a similarly vast total conversion for the enduring Stalker: Call of Pripyat.
Call of Chernobyl is a "freeplay" mod, which means it strips away most of the Call of Pripyat's plot and linear progression in favour of the ability to roam anywhere and extra focus on the game's survival elements. The latter includes optional additions like sleep deprivation to contend with, but the mod makes many other changes, including expanding the world map, overhauling the AI and A-Life systems, and much more. It also contains all the maps from all Stalker games - Shadow of Chernobyl, Clear Sky, and Call of Pripyat - each remade to fit the mechanics of the mod, with new shelters to sleep in, traders to buy vodka from, and so on.
Apparently there was less than one percent difference in voting numbers between Call of Chernobyl and Enderal, so both are clearly pretty good. You can find the full top ten mods here, which includes other games such as Hearts of Iron IV: The Great War in third place and Brutal Doom 64 in fifth.
Voting has also come to an end for IndieDB's indie game of the year. The list tends to highlight games I'm already familiar with so is less interesting to me, but you can find the top ten - including first placed RimWorld - over here.