I think I'm measuring my top twenty more off of fond memories and nostalgia (nostalgia being the big theme for most of GOG anyways), and rank games off that (with the exception of one or two titles, but I'll explain those).
20 DoomRL (pc): Not really much of an old game, but it harkens to not only the old rogue game elements, but a classic shooter in-itself. The new .9.9.6 patch got 10x better with gorgeous tilesets.
19 Dragon Quest VIII (PS2): Again, not quite an "old" game by my standards, but it pulls from a lot of old, classic Dragon Quest elements and provides an insanely large, deep world to explore in a JRPG format. Definitely worth the ten bucks I spent to buy it.
18 Final Fantasy IX (PS1): Hard to believe this game is twelve year's old now, but I remember loving this game when it came out in my junior year of high school. It had the classic NES/SNES FF elements that I loved. Definitely a fan service title, but done so well I'll still play it totday.
17 Castlevania SotN (PS1): Aahhhhhh... How blown away was my mind when I got this game. I had no clue what I was getting when I purchased this title, nor would I know how much time would be lost playing it.
16 Warcraft III (excluding expansion) (pc): I was floored by the CG when this game came out, I loved how they injected small elements of RPG into the game and dug the hell out of the story. True, it was definitely somewhat of a place holder/intro to lead to WoW, but it was still good. I think I remember more of when I got my first graphics card and how it blew this game outta the water.
15 Punisher (NES): LJN has made nothing but horrible games that made me cry as a kid, yet this is one title that was amazing. Not only did they make a great shooting game, but they actually did something new and innovative that worked rather well. STill hard as balls.
14 Contra III (SNES): I'm pretty sure "this" was the best Contra game ever made. So gorgeous looking, lot's of great elements taking advantage of the reknown "mode 7" and punishing us in the way only a Contra game could, yet still wanting more.
13 Gauntlet (C64): This is one of several games me and my dad played together, so it's definitely a special title. I remember me and him getting to a tough spot that required a little coordination before hand. My dad advised me to hit the spawn points from whence the monster's were spawning while he'd kill the monsters. Brilliant plan, and like any good plan, fell apart the moment he was relying on a six year old to execute. Meh, shit happens.
12 Friday the 13th (NES): Okay, this is a bad game. It really is, but why is it on my list? Cause it scared the shit out of this seven year old when he played it! I never played it by myself, always at my friend's house and always when someone was around. But those pop scares we got while playing it was amazing and sharing the experience with my best friend at the time makes me sigh in a very nostalgic sense.
11 Morrowind (pc): It took my third run through before I ever fully got hooked. What an alien looking world they created, and gave to a great gaming experience. I don't think Betheseda will ever be able to capture me like that again.
10 TMNT (NES): I hate this game. I hate every bit about it, I hate the dam level the most. The one game me and my friends could NEVER beat, but yet still love. Nothing funnier than school yard conversations where everyone gripes about the stupid dam level.
09 SimCity (PC): My first lesson in fiscal responsibility. "What do you mean I can't build three football stadium?" This was another title I played with my dad and even got my mom into it. It was good times.
08 Gettysburg (PC): What a beautiful game, but what made this great, was playing it with my grandfather. 'nuff said.
07 Mortal Kombat (SNES/Genesis): The one thing that sticks out most for me playing this game, is remembering how I met all these kids for the first time and never knew them, but within a matter of minutes we were all tight after a few rounds playing this game. Not one of the ten of us knew how to execute a finishing move.
06 Final Fantasy II (snes): First JRPG (but not the first RPG), I played. I had know idea what I was doing and me and my friends were oblivious to the fact of how the game works. I figure if I just keep selecting "fight" I'll win the game...what's this "magic" stuff? Besides that portion, it's just another classic staple in my childhood memories.
05 Wolfenstein 3D (SNES): I have to say the SNES version is slightly superior to the PC. The game's about half as long as the PC verion, but more textues, a flame thrower AND a rocket launcher. Yea, it's censored quite a bit, but as a kid I didn't notice nor did I care. It was just a fun damn game.
04 Ultimate Doom (pc): I remember me and my dad playing this title quite a bit. Holy hell, when I got to the third or fourth stage in the first Episode where the pinky demon shows up, scared the crap out of me. Nothing more nerve racking then the ambient sound of them snarlying.
03 Super Mario Bros 3 (NES): This is definitely the baseline of, not only my gaming experiences as a kid, but many others as well. Nothing cooler than finding the hidden whistles, overcoming the bosses, wishing you has a sweet, wooden airship and dying from the game, a lot. What makes this game better was that my old man liked this title a lot and it was the reason why I got an SNES and Super Mario World (so he could play it).
02 Ultima 6 (PC): My first RPG. Wow I was blown away. I never realized how interactive the world was at. What a fully living, interactive world. People had schedules, a night/day rotation, I could interact with practically every element of the game. This game was ground breaking, and I was floored that it took six 5 1/4 floppy disks, SIX! Me and my dad never really played the game so much as wandered around. Just so damn amazing.
01 Final Fantasy III (snes): There will never be a game that will capture my heart like this game did. Such a huge cast of characters, each with a story to flush out, each with a some unqiue ability to bring to the game. The setting was awe-inspiring, with such an amazing steam-punk style. The monsters were so beautifully drawn, with such detail. The music, just...stunning. Best, damn game, ever.