The Top 3 games I have played are not necessarily my top 3 favorite video games. The top 3 games that I have played though happen to be these.
1. Ogre Battle: The March of the Black Queen
I am usually turned off by strategy games due to the pacing that they have. Sure I guess for some it is nice to be controlling multiple different people at a time, equipping all of them, and then sending them to do battle with your commands, but that becomes a bore to me, especially since most of them tend to rely on chance. However I got this game for Christmas, played it and loved it. It has all of those things I mentioned above except for the chance aspect, because you have to manage different units who will attack differently depending on their placement in a unit. Plus battles are done like a typical RPG, but moves much quicker. That's what I like, the speed of the game and the enemies. If you're a fan of XCOM: Enemy Unknown then you might enjoy this.
2. Chrono Trigger
Hands down, the best turn-based JRPG of all time. Final Fantasy VII fans can go suck a fuck. The story, the characters, the graphics, the music, all of it is just wonderful. The gameplay is the shining jewel though. Combining attacks, getting tricky with the enemies, and moving as fast as you can to kill the enemy while keeping yourself healed. This game would force you to multitask and use time travel. Truly the best JRPG and one of the best video games of all time.
3. The Legend of Zelda: Majora's Mask
Although my favorite Zelda game is The Legend of Zelda: Twilight Princess, I do have to say though that Majora's Mask is the superior game in terms of best. The use of masks, the people of Clock Town, and the areas of Termina. The story was so dark, but it wasn't really pushed on you. It had its funny moments and it has its sad moments as well. You have the gameplay from Ocarina of Time, but it felt fresh and it feels a bit smoother as well. Seeing as useless items now have more uses to you.