Depends. What do you mean with childhood? We got our 386SX when I was about 12 years old, in 1992. Not an easy question. I'll probably have to choose between Wolfenstein 3D, Doom and Doom 2. Which is almost impossible. Doom 2 was the better game, Wolfenstein 3D had the most impact. You have to remember: it's early 90's. You are playing games like Alley Cat, EgaWalls, Prince Of Persia, LodeRunner, etc...I remember the day: our dad bought the latest copy of PC Format with the usual demodisks. And there it was: the shareware version of Wolfenstein 3D. Our dad installed it and told us to eat our dinner first, because this was going to be good And it sure was. Even at 12 years of age, we knew this game was a going to be a milestone. I'm very grateful that we lived through all those moments, and witnessed it first hand: Wolfenstein, Doom, Quake, Duke Nukem 3D, the Jedi games, X-Wing, Wing Commander, Half Life, Unreal... Those times will never come back.
Started on Commodore 84 then continued playing mostly on Amiga 500 so I would consider games on those systems my childhood games.
And I loved Brian the Lion, Superfrog and Zool on Amiga for its platforming goodness.
You know, somebody is selling a sealed copy of Prince Of Persia on ebay, for around 5000 dollars LOL But yeah. Great game, difficult, but satisfying when you reach the end. Prince of Persia 2 was better: the same, but more. More scenery, more levels, more enemies, sound effects, music...it was the perfect side scroller at that time. I always liked the mystery that came with those 2 games.
For me, it's probably Rollercoaster Tycoon. 10-year old me had no idea what good park management actually entailed, of course, but darnit if I didn't enjoy building the most amazing rollercoasters and seeing how high I could get those enjoyment scores.
Another great contender is Descent 2, the 6DOF shooter with the rocking soundtrack. My stepfather had a HOTAS even then and I remember vividly the joy I would get from blasting through those endless robot-infested mines at breakneck speed, firing twin gauss cannons and launching earthshaker missiles. Good luck, material defender!
And lastly.. Carmageddon 2. We definitely weren't supposed to be playing that but the violence was so ridiculous, so over the top and so obviously fake and cartoonish that you just couldn't help but laugh. And this game provided laughs in spades! It was also the very first 3DFX game I ever played and man, did that look amazing! This and Turok were the poster children for graphics acceleration back then.
So many favorites, but if I really had to pick just one, it would have to be Mega Man 2. I bought the game with my own "hard-earned" money and I had a blast playing it. The music is what I remember the most. as the soundtrack is superb and feels quite unique compared to a lot from the same decade. Pretty sure If I ever heard the same soundtrack 50+ years from now, I would easily say: ah, Mega Man! Graphics, combat, bosses/skill are other parts of the game that really clicked for me.
Childhood games? Hmmmm, well when I was 10 it was all about Commander Keen 4 - Secret of the Oracle, Keen 3.5 Keen Dreams, Major Stryker, Catacombs Abyss, Crystal Caves, Secret Agent, Duke Nukem, Dune 2 The Building of a Dynasty, New York Warriors, and Wolfenstein 3D. There was no best, simply a ton of great full version and shareware games.
In 1994 that all changed when Looking Glass Studios released System Shock, and 26 years later it is my number one game of all time.
Keen 1, Keen Dreams, and Keen 4 were played and completed by me in those early 90's. It was only later did I finally get access to Keen 2,3, 5, and 6 - Aliens Ate my Babysitter. All completed but I still haven't finished Keen 2 or Keen 3.