Well, I decided to update my top 50 list and huge changes have been made, especially in the top 10.
I will post one every day, going from 50 to 1. I will also add explanations why the game's on the list and why it's not higher.

First of all, the honourable mentions: Dragon Warrior (NES), The Legend of Zelda (NES), Kid Icarus (NES), Crash Bandicoot 3 (PS1), Xenogears (PS1), GTA San Andreas (PS2), Dragon Quest V (SNES), Dragon Quest VIII (PS2), Tales of Symphonia (GC), Fire Emblem (GBA), Knights of th Old Republic (Xbox), Warcraft 3 (PC), Kingdom Hearts 2 (PS2), Starcraft (PC), Panzer Dragoon Saga (Saturn), NiGHTS (Saturn), Devil May Cry (PS2), Resident Evil 4 (GC/PS2/Wii), Streets of Rage 2 (GEN), System Shock 2 (PC), Deus Ex (PC), Perfect Dark (N64), Final Fantasy Tactics (PS1)
I know, quite a lot, but these were the games of the long list that didn't make the final cut. :(

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50. Final Fantasy V (SNES)

Why on the list?
- This FF was never released outside of Japan, which is a shame. It had really fun gameplay with the job system. Rapid Fire/Spellblade FTW!
- This FF featured one of the most memorable villains, and probably the funniest: Gilgamesh. He's supposed to be a mighty general, but is actually a coward and runs off during every battle you have with him. At a certain moment he thinks he's just found the legendary sword Excalibur and fights you with it. Turns out it's actually a worthless copy that does 1 damage. In the end he chooses your side and sacrifices himself.
He also has one of the best FF themes of all time: Battle on the Big Bridge.

"Now we fight like men! And ladies! And ladies who dress like men! For gilgamesh it's MORPHING TIME!" :)

Why not higher?
- Apart from Gilgamesh the characters are rather bland, none of the heroes really stands out.
- The other SNES FFs were simply better.