Tagging for now. My #1 is definitely Gravity Rush though. It has an amazing soundtrack imo.

1. Legend of Zelda Wind Waker
2. Persona 5
3. Xenoblade Chronicles
4. Mario Kart 8
5. Undertale
6. GGXrd Rev 2
7. Nier Automata
8. Bastion
9. Pokemon Soulsilver
10. Super Mario 64

This is terribly hard.

Just Zelda alone; I'd put The Wind Waker, Majora's Mask and A Link Between Worlds all in my top 10, but to choose only one... I'll come up with a list soon though.

1 Pitfall II
2 Europa Universalis III
3 F-Zero X
4 Mega Man X
5 Shovel Knight
6 Victoria II
7 Zelda Ocarina of Time
8 Crusader Kings II
9 Hearts of Iron III
10 Minecraft

reporting you for shit taste 

1. Shadow of the Colossus
2. Castlevania: Symphony of the Night
3. Silent Hill 2
4. Streets of Rage 2
5. Journey
6. Vagrant Story
7. Chrono Cross
8. Final Fantasy VIII
9. Ninja Gaiden 2 (NES)
10. ICO

I almost put your #1 on my list.  I remember the music being good, but more importantly it is the first game I remember having actual music other than a few seconds at the opening or something similarly minor.

For the sake of transparency I'll post my top 10 here as well.

1. Final Fantasy IX

2. Total Annihilation

3. Shadow of the Colossus

4. Dark Souls

5. Nier

6. The Legend of Heroes: Trails of Cold Steel SC

7. Lost Odyssey

8. Okami

9. Chrono Cross

10. Mega Man 2

Here's another quick update on where the top 50 is right now.
-43 people have left their vote, with 238 different games receiving at least one mention
-18 games are sitting at just one point at the moment.
-8 games have ten points received from being somebody's #1, but have not received any additional votes from anyone
-The cutoff point to get into the top 50 is 11 points right now.